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1. Male attractiveness is subjective to exposure to males of different attractiveness in fruit flies

Author: Laure-Anne Poissonnier, Etienne Danchin, and Guillaume Isabel
Subjects: Medicine, Science
Abstract: Abstract Mate choice is a crucial decision in any animal. In terms of fitness, the best mate is the one that leads to the most abundant and productive offspring. Pairing with a low-quality mate would reduce fitness, generating selection for accurate and subtle mate choice in all animal species. Hence, mate choice is expected to be highly context dependent, and should depend on other potential options. For instance, a medium-quality male can constitute the best option when all other males are in poorer condition, but not when there are better-quality males available. Therefore, animals are predicted to gather information about their social context and adapt their mate choice to it. Here, we report on experiments in which we manipulated the social environment of females of Drosophila melanogaster and found that after encountering a high or a low-quality male, they take more or less time to accept copulation with another male, suggesting that females adapt their mating strategy to their social context. We also report on a similar effect in D. biarmiceps. Thus, male attractiveness appears to depend on the quality of recently met males, suggesting that male attractiveness is subjective, indicating plastic and context dependent mate choice.
Published: 2024
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2. A social learning primacy trend in mate-copying: an experiment in Drosophila melanogaster

Author: Ricardo Santiago Araújo, Sabine Nöbel, Diogo F. Antunes, Etienne Danchin, and Guillaume Isabel
Subjects: observational learning, social learning, learning plasticity, reversal learning, mate-copying, mate choice, Science
Abstract: Social learning is learning from the observation of how others interact with the environment. However, in nature, individuals often need to process serial social information and may favour either the most recent information (recency bias), constantly updating knowledge to match the environment, or the information that appeared first in the series (primacy bias), which may slow down adjustment to environmental change. Mate-copying is a widespread form of social learning in a mate choice context related to conformity in mate choice, and where a naive individual develops a preference for a given mate (or mate phenotype) seen being chosen by conspecifics. Mate-copying is documented in most vertebrate taxa and in the fruit fly Drosophila melanogaster. Here, we tested experimentally whether female fruit flies show a primacy or a recency bias by presenting pictures of a female copulating with one of two contrastingly coloured male phenotypes. We found that after two sequential contradictory demonstrations, females show a tendency to prefer males of the phenotype preferred in the first demonstration, suggesting that mate-copying in D. melanogaster is not based on the most recently observed mating and may be influenced by a form of primacy bias.
Published: 2024
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3. Mate copying requires the coincidence detector Rutabaga in the mushroom bodies of Drosophila melanogaster

Author: Sabine Nöbel, Etienne Danchin, and Guillaume Isabel
Subjects: Biological sciences, Neurogenetics, Neuroscience, Behavioral neuroscience, Science
Abstract: Summary: Mate choice constitutes a major fitness-affecting decision often involving social learning leading to copying the preference of other individuals (i.e., mate copying). While mate copying exists in many taxa, its underlying neurobiological mechanisms remain virtually unknown. Here, we show in Drosophila melanogaster that the rutabaga gene is necessary to support mate copying. Rutabaga encodes an adenylyl cyclase (AC-Rut+) acting as a coincidence detector in associative learning. Since the brain localization requirements for AC-Rut+ expression differ in classical and operant learning, we determine the functional localization of AC-Rut+ for mate copying by artificially rescuing the expression of AC-Rut+ in neural subsets of a rutabaga mutant. We found that AC-Rut+ has to be expressed in the mushroom bodies’ Kenyon cells (KCs), specifically in the γ-KCs subset. Thus, this form of discriminative social learning requires the same KCs as non-social Pavlovian learning, suggesting that pathways of social and asocial learning overlap significantly.
Published: 2023
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4. A simple ATAC-seq protocol for population epigenetics [version 2; peer review: 2 approved]

Author: Ronaldo de Carvalho Augusto, Oliver Rey, Céline Cosseau, Cristian Chaparro, Jérémie Vidal-Dupiol, Jean-François Allienne, David Duval, Silvain Pinaud, Sina Tönges, Ranja Andriantsoa, Emilien Luquet, Fabien Aubret, Mamadou Dia Sow, Patrice David, Vicki Thomson, Dominique Joly, Mariana Gomes Lima, Déborah Federico, Etienne Danchin, Aki Minoda, and Christoph Grunau
Subjects: Medicine, Science
Abstract: We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.
Published: 2021
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5. Dopamine and Serotonin Are Both Required for Mate-Copying in Drosophila melanogaster

Author: Magdalena Monier, Sabine Nöbel, Etienne Danchin, and Guillaume Isabel
Subjects: fruit fly, mate choice, social learning, social memory, 3-iodotyrosine (3-IY), DL-para-chlorophenylalanine (PCPA), Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Mate-copying is a form of social learning in which the mate-choice decision of an individual (often a female) is influenced by the mate-choice of conspecifics. Drosophila melanogaster females are known to perform such social learning, and in particular, to mate-copy after a single observation of one conspecific female mating with a male of one phenotype, while the other male phenotype is rejected. Here, we show that this form of social learning is dependent on serotonin and dopamine. Using a pharmacological approach, we reduced dopamine or serotonin synthesis in adult virgin females with 3-iodotyrosine (3-IY) and DL-para-chlorophenylalanine (PCPA), respectively, and then tested their mate-copying performance. We found that, while control females without drug treatment copied the choice of the demonstrator, drug-treated females with reduced dopamine or serotonin chose randomly. To ensure the specificity of the drugs, the direct precursors of the neurotransmitters, either the dopamine precursor L-3,4-dihydroxyphenylalanine (L-DOPA) or the serotonin precursor 5-L-hydroxytryptophan (5-HTP) were given together with the drug, (respectively 3-IY and PCPA) resulting in a full rescue of the mate-copying defects. This indicates that dopamine and serotonin are both required for mate-copying. These results give a first insight into the mechanistic pathway underlying this form of social learning in D. melanogaster.
Published: 2019
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6. Overwintering aggregations are part of Hippodamia undecimnotata's (Coleoptera: Coccinellidae) mating system.

Author: Eline Catherine Susset, Jean-Louis Hemptinne, Etienne Danchin, and Alexandra Magro
Subjects: Medicine, Science
Abstract: Aggregation during diapause is a common phenomenon in arthropods that nevertheless remains poorly understood. The most commonly claimed benefit is that survival is higher in aggregations but animal aggregations could also be driven by sexual selection. In this perspective, we investigated whether aggregations in insects could be part of their mating system. We studied the overwintering aggregations of the ladybird Hippodamia undecimnotata (Schneider), an aphidophagous species from Southern and Eastern Europe as well as Asia. We collected ladybirds at three aggregation sites in Southwest France, during two overwintering periods (2013-2014 and 2014-2015). We checked their reproductive status by counting the viable sperm cells in the sperm storage organs of both males and females, and by assessing the ovarian status of females. We also investigated if mating behaviour occurred in these aggregations. We found that males have a high quantity of viable sperm cells (70-95%) in their reproductive organs throughout the overwintering periods. In contrast, although most females (85-95%) had empty spermatheca at the onset of the aggregations in autumn, the majority (65-91%) had numerous viable sperm in their spermatheca at the time of dispersal from the aggregation in early spring. Furthermore, frequent copulations were observed towards the end of the overwintering period, few weeks before dispersal. These results suggest that finding sexual mates may have been involved in overwintering aggregations in H. undecimnotata.
Published: 2018
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7. The double pedigree: a method for studying culturally and genetically inherited behavior in tandem.

Author: Etienne Danchin, Benoit Pujol, and Richard H Wagner
Subjects: Medicine, Science
Abstract: Transgenerational sources of biological variation have been at the center of evolutionary studies ever since Darwin and Wallace identified natural selection. This is because evolution can only operate on traits whose variation is transmitted, i.e. traits that are heritable. The discovery of genetic inheritance has led to a semantic shift, resulting in the tendency to consider that only genes are inherited across generations. Today, however, concepts of heredity are being broadened again to integrate the accruing evidence of non-genetic inheritance, and many evolutionary biologists are calling for the inclusion of non-genetic inheritance into an inclusive evolutionary synthesis. Here, we focus on social heredity and its role in the inheritance of behavioral traits. We discuss quantitative genetics methods that might allow us to disentangle genetic and non-genetic transmission in natural populations with known pedigrees. We then propose an experimental design based on cross-fostering among animal cultures, environments and families that has the potential to partition inherited phenotypic variation into socially (i.e. culturally) and genetically inherited components. This approach builds towards a new conceptual framework based on the use of an extended version of the animal model of quantitative genetics to integrate genetic and cultural components of behavioral inheritance.
Published: 2013
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8. Incestuous sisters: mate preference for brothers over unrelated males in Drosophila melanogaster.

Author: Adeline Loyau, Jérémie H Cornuau, Jean Clobert, and Etienne Danchin
Subjects: Medicine, Science
Abstract: The literature is full of examples of inbreeding avoidance, while recent mathematical models predict that inbreeding tolerance or even inbreeding preference should be expected under several realistic conditions like e.g. polygyny. We investigated male and female mate preferences with respect to relatedness in the fruit fly D. melanogaster. Experiments offered the choice between a first order relative (full-sibling or parent) and an unrelated individual with the same age and mating history. We found that females significantly preferred mating with their brothers, thus supporting inbreeding preference. Moreover, females did not avoid mating with their fathers, and males did not avoid mating with their sisters, thus supporting inbreeding tolerance. Our experiments therefore add empirical evidence for inbreeding preference, which strengthens the prediction that inbreeding tolerance and preference can evolve under specific circumstances through the positive effects on inclusive fitness.
Published: 2012
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9. Unzipped genome assemblies of polyploid root-knot nematodes reveal new kinds of unilateral composite telomeric repeats

Author: Etienne Danchin, Ana Paula Zotta Mota, Georgios Koutsovoulos, Laetitia Perfus-Barbeoch, Evelin Despot-Slade, Karine Labadie, Jean Marc Aury, Karine Robbe-Sermesant, Marc Bailly-Bechet, Caroline Belser, Arthur Pere, Corinne Rancurel, Djampa Kozlowski, Rahim Hassanaly-Goulamhoussen, Martine Da Rocha, Benjamin Noel, Nevenka Meštrović, and Patrick Wincker
Abstract: Using long read sequencing we have assembled and unzipped the genomes of Meloidogyne incognita, M. javanica and M. arenaria, the three most devastating plant-parasitic nematodes at unparalleled contiguity. The telomeric repeat (TTAGGC)n, evolutionarily conserved in nematodes, was not found in these genomes. Furthermore, no evidence for a telomerase enzyme or for orthologs of C. elegans telomere-associated proteins could be found. Instead, we identified species-specific composite repeats enriched at one extremity of contigs. These repeats were G-rich, oriented and transcribed, similarly to known telomeric repeats. Using fluorescent in situ hybridization, we confirmed these repeats had telomeric location at one single end of M. incognita chromosomes. The discovery of a new kind of telomeric repeat in these species highlights the evolutionary diversity of chromosome protection systems despite their central roles in senescence, aging and chromosome integrity and opens new perspectives towards the development of more specific control methods against these pests.
Published: 2023

10. Conformity in mate choice, the overlooked social component of animal and human culture

Author: Sabine Nöbel, Antoine Jacquet, Guillaume Isabel, Arnaud Pocheville, Paul Seabright, and Etienne Danchin
Subjects: General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology
Abstract: Although conformity as a major driver for human cultural evolution is a well-accepted and intensely studied phenomenon, its importance for non-human animal culture has been largely overlooked until recently. This limited for decades the possibility of studying the roots of human culture. Here, we provide a historical review of the study of conformity in both humans and non-human animals. We identify gaps in knowledge and propose an evolutionary route towards the sophisticated cultural processes that characterize humanity. A landmark in the study of conformity is Solomon Asch's famous experiment on humans in 1955. By contrast, interest in conformity among evolutionary biologists has only become salient since the turn of the new millennium. A striking result of our review is that, although studies of conformity have examined many biological contexts, only one looked at mate choice. This is surprising because mate choice is probably the only context in which conformity has self-reinforcing advantages across generations. Within a metapopulation, i.e. a group of subpopulations connected by dispersing individuals, dispersers able to conform to the local preference for a given type of mate have a strong and multigenerational fitness advantage. This is because once females within one subpopulation locally show a bias for one type of males, immigrant females who do not conform to the local trend have sons, grandsons, etc. of the non-preferred phenotype, which negatively and cumulatively affects fitness over generations in a process reminiscent of the Fisher runaway process. This led us to suggest a sex-driven origin of conformity, indicating a possible evolutionary route towards animal and human culture that is rooted in the basic, and thus ancient, social constraints acting on mating preferences within a metapopulation. In a generic model, we show that dispersal among subpopulations within a metapopulation can effectively maintain independent Fisher runaway processes within subpopulations, while favouring the evolution of social learning and conformity at the metapopulation scale; both being essential for the evolution of long-lasting local traditions. The proposed evolutionary route to social learning and conformity casts surprising light on one of the major processes that much later participated in making us human. We further highlight several research avenues to define the spectrum of conformity better, and to account for its complexity. Future studies of conformity should incorporate experimental manipulation of group majority. We also encourage the study of potential links between conformity and mate copying, animal aggregations, and collective actions. Moreover, validation of the sex-driven origin of conformity will rest on the capacity of human and evolutionary sciences to investigate jointly the origin of social learning and conformity. This constitutes a stimulating common agenda and militates for a rapprochement between these two currently largely independent research areas.
Published: 2022

11. The importance of population heterogeneities in detecting social learning as the foundation of animal cultural transmission

Author: Sabine Nöbel, Xiaobo Wang, Laurine Talvard, Juliette Tariel, Maëva Lille, Julien Cucherousset, Myriam Roussigné, Etienne Danchin, Institute for Advanced Study in Toulouse (IAST), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie Intégrative (CBI), and Université Toulouse III - Paul Sabatier (UT3)
Subjects: Male, General Immunology and Microbiology, Reproduction, General Medicine, Mating Preference, Animal, General Biochemistry, Genetics and Molecular Biology, Cyprinodontiformes, social learning, [SCCO]Cognitive science, personality, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animals, Gambusia holbrooki, mosquitofish, Female, mate copying, General Agricultural and Biological Sciences, B- ECONOMIE ET FINANCE, General Environmental Science
Abstract: High levels of within-population behavioural variation can have drastic demographic consequences, thus changing the evolutionary fate of populations. A major source of within-population heterogeneity is personality. Nonetheless, it is still relatively rarely accounted for in social learning studies that constitute the most basic process of cultural transmission. Here, we performed in female mosquitofish ( Gambusia holbrooki ) a social learning experiment in the context of mate choice, a situation called mate copying (MC), and for which there is strong evidence that it can lead to the emergence of persistent traditions of preferring a given male phenotype. When accounting for the global tendency of females to prefer larger males but ignoring differences in personality, we detected no evidence for MC. However, when accounting for the bold–shy dichotomy, we found that bold females did not show any evidence for MC, while shy females showed significant amounts of MC. This illustrates how the presence of variation in personality can hamper our capacity to detect MC. We conclude that MC may be more widespread than we thought because many studies ignored the presence of within-population heterogeneities.
Published: 2022

12. Spying on your neighbours? Social information affects timing of breeding and stress hormone levels in a colonial seabird

Author: Etienne Danchin, Scott A. Hatch, Thomas Merkling, Sarah Leclaire, Olivier Chastel, Anika Immer, Pierrick Blanchard, Laboratoire Evolution & Diversite Biologique UMR 5174 [Toulouse, France], CNRS, UPS, IRD, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, Mechanism (biology), Egg mass, Reproduction (economics), Context (language use), Experimental approach, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, 030104 developmental biology, Public information, Animal ecology, biology.animal, [SDE]Environmental Sciences, Seabird, Baseline (configuration management), Social information, Glucocorticoids, Personally identifiable information, Timing of reproduction, Ecology, Evolution, Behavior and Systematics, Demography
Abstract: International audience; A good overlap between offspring energetic requirements and availability of resources is required for successful reproduction. Accordingly, individuals from numerous species fine-tune their timing of breeding by integrating cues that predict environmental conditions during the offspring period. Besides acquiring information from their direct interaction with the environment (personal information), individuals can integrate information by observing the behaviours or performance of others (social information). The use of social information is often beneficial because the accumulated knowledge of conspecifics may represent a source of information more reliable than the intrinsically more limited personal information. However, although social information constitutes the major source of information in a wide range of contexts, studies investigating its use in the context of timing of breeding are scarce. We investigated whether black-legged kittiwakes (Rissa tridactyla) used social information to adjust the timing of egg-laying. We manipulated social information using a food-supplementation experiment, known to advance kittiwakes' reproductive phenology. We expected food-supplemented and unsupplemented pairs to delay and advance, respectively, their timing of laying when surrounded by a majority of neighbours from the opposite food-treatment. However, both unsupplemented and food-supplemented kittiwakes delayed egg-laying when surrounded by a higher proportion of neighbours from the opposite food-treatment. This result shows that kittiwakes use social information to time egg-laying, but that it is not used to match the seasonal peak of food availability. We suggest that when social and personal cues give contradictory environmental information, individuals may benefit from delaying laying to gather more information to make better decisions about investment into eggs. Further, we explored a potential proximate mechanism for the pattern we report. We show that baseline corticosterone, known to mediate reproductive decisions, was lower in unsupplemented females facing a higher proportion of food-supplemented neighbours. Altogether, our results suggest that to fine-tune their timing of laying, kittiwakes use complex decision-making processes in which social and personal information interplay.
Published: 2021

13. No evidence for mate copying in Danio rerio

Author: Sabine Nöbel, Xiaobo Wang, Marion Cristante, Marine Guëll, Juliette Tariel, Etienne Danchin, Myriam Roussigné, Institute for Advanced Study in Toulouse (IAST), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre de biologie du développement (CBD), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-13-BSV7-0007,SOC-H2,L'hérédité sociale comme processus de biodiversité(2013), and ANR-10-LABX-1401,'Investissements d'avenir',ANR-10-LABX-14-01
Subjects: social learning, Behavioral Neuroscience, personality, [SDV]Life Sciences [q-bio], public information, Animal Science and Zoology, General Medicine, mate choice, mate copying, Public information Social learning Mate choice Mate copying Personality Zebrafish, zebrafish
Abstract: International audience; The zebrafish Danio rerio is an important model organism, but little is known about its mating preferences and how these are influenced by personality traits like boldness. In this study, we tested two strains of zebrafish and addressed whether females used social information to build a mating preference, a behavior called mate copying, and whether this social learning was affected by boldness. Thus, we provided positive social information for small males to test whether female zebrafish changed their mate preference after observing a pair of a small and a large male with a demonstrator female next to the small one. After that, we tested the observer female in a test maze to evaluate boldness. We found no significant evidence for mate copying as females did not change their preference for the small male after witnessing the large male alone and the small male interacting with another female and chose consistently larger males in a control without opportunity to copy. Whether the female was defined as shy or bold had no effect on mate copying. We conclude that mate copying is probably inexistent or only relatively weak in this species.
Published: 2023

14. Evolutionarily conserved plant genes responsive to root-knot nematodes identified by comparative genomics

Author: Diana Fernandez, Bruno Paes de Melo, Maria Fatima Grossi-de-Sa, Etienne Danchin, Maria E. Lisei de Sa, Ana Cristina Miranda Brasileiro, Erika V.S. Albuquerque, Mario A. P. Saraiva, Patricia Messenberg Guimaraes, Fabricio B. M. Arraes, Anne-Sophie Petitot, Ana Paula Zotta Mota, Priscila Grynberg, Embrapa Recursos Genéticos e Biotecnologia [Brasília], Departamento de Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Departamento de Bioquímica e Biologia Molecular/Bioagro, Universidade Federal de Vicosa (UFV), Empresa de Pesquisa Agropecuária de Minas Gerais (EPAMIG), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 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), Universidade Católica de Brasília (UCB), CAPES, National Council for Scientific and Technological Development (CNPq) 400328/2012-7, Agropolis Fondation (Montpellier, France) 002/14, Embrapa, CAPES 1402-004, INCT PlantStress Biotech 465480/2014-4, FAPDF-Distrito Federal Research Foundation 193001265/2017, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), and Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
Subjects: Crops, Agricultural, 0106 biological sciences, 0301 basic medicine, Arachis, Meloidogyne, Genotype, Oryza glaberrima, Coffee, 01 natural sciences, Transcriptome, 03 medical and health sciences, Gene Expression Regulation, Plant, Genetics, Plant defense against herbivory, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Plant Immunity, Tylenchoidea, Molecular Biology, Gene, Disease Resistance, Plant Diseases, Plant Proteins, 2. Zero hunger, Comparative genomics, Plant evolution, biology, food and beverages, Oryza, Genomics, General Medicine, 15. Life on land, biology.organism_classification, 030104 developmental biology, Peptide transport, Host-Pathogen Interactions, Rice, Soybeans, Soybean, 010606 plant biology & botany
Abstract: Root-knot nematodes (RKNs, genus Meloidogyne) affect a large number of crops causing severe yield losses worldwide, more specifically in tropical and sub-tropical regions. Several plant species display high resistance levels to Meloidogyne, but a general view of the plant immune molecular responses underlying resistance to RKNs is still lacking. Combining comparative genomics with differential gene expression analysis may allow the identification of widely conserved plant genes involved in RKN resistance. To identify genes that are evolutionary conserved across plant species, we used OrthoFinder to compared the predicted proteome of 22 plant species, including important crops, spanning 214 Myr of plant evolution. Overall, we identified 35,238 protein orthogroups, of which 6,132 were evolutionarily conserved and universal to all the 22 plant species (PLAnts Common Orthogroups-PLACO). To identify host genes responsive to RKN infection, we analyzed the RNA-seq transcriptome data from RKN-resistant genotypes of a peanut wild relative (Arachis stenosperma), coffee (Coffea arabica L.), soybean (Glycine max L.), and African rice (Oryza glaberrima Steud.) challenged by Meloidogyne spp. using EdgeR and DESeq tools, and we found 2,597 (O. glaberrima), 743 (C. arabica), 665 (A. stenosperma), and 653 (G. max) differentially expressed genes (DEGs) during the resistance response to the nematode. DEGs' classification into the previously characterized 35,238 protein orthogroups allowed identifying 17 orthogroups containing at least one DEG of each resistant Arachis, coffee, soybean, and rice genotype analyzed. Orthogroups contain 364 DEGs related to signaling, secondary metabolite production, cell wall-related functions, peptide transport, transcription regulation, and plant defense, thus revealing evolutionarily conserved RKN-responsive genes. Interestingly, the 17 DEGs-containing orthogroups (belonging to the PLACO) were also universal to the 22 plant species studied, suggesting that these core genes may be involved in ancestrally conserved immune responses triggered by RKN infection. The comparative genomic approach that we used here represents a promising predictive tool for the identification of other core plant defense-related genes of broad interest that are involved in different plant-pathogen interactions.
Published: 2020

15. More than Fifty Shades of Epigenetics for the Study of Early in Life Effects in Medicine, Ecology, and Evolution

Author: Etienne Danchin
Published: 2022

16. MHC-II distance between parents predicts sex allocation decisions in a genetically monogamous bird

Author: Thomas Merkling, Etienne Danchin, Pierrick Blanchard, Maxime Pineaux, Sarah Leclaire, Scott A. Hatch, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Institute for Searbird Research and Conservation
Subjects: Evolutionary biology, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animal Science and Zoology, Biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics, Sex allocation, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction
Abstract: Theory predicts that parental heritable characteristics should shape sex allocation decisions when their effects on reproduction or survival are offspring sex-dependent. Numerous studies have questioned to what extent characteristics displayed by one of the parents matched theoretical expectations. This contrasts with the handful of studies that investigated whether compatibility between parents could also trigger selective pressures for sex allocation adjustments. We studied the genetically monogamous black-legged kittiwake (Rissa tridactyla), where previous data revealed that female chicks suffered higher fitness costs from low diversity at genes of the major histocompatibility complex (MHC) than male chicks. We predicted, and found in our dataset, that MHC-similar parents, producing low MHC-diverse offspring, should avoid the production of females. The relation between MHC-distance between parents (i.e. the functional distinctness of their MHC alleles) and offspring sex was not linear, such that MHC-dissimilar parents also overproduced sons. Overall, our results suggest that the genetically monogamous black-legged kittiwake parents flexibly adapt their reproduction and circumvent the costs of suboptimal pairing by manipulating offspring sex.
Published: 2022

17. Signatures of the Evolution of Parthenogenesis and Cryptobiosis in the Genomes of Panagrolaimid Nematodes

Author: Philipp H. Schiffer, Michael A. S. Thorne, Michael Kroiher, Georgina O’Mahony, Simon Wong, Aleksandra Marconi, Ann M. Burnell, Elizabeth A. Martínez-Salazar, Mark Blaxter, Ilona Dix, Urmi Trivedi, Etienne Danchin, Bridget A. Culleton, Thomas Wiehe, Christopher J. Creevey, Gary Stier, Einhard Schierenberg, Corinne Rancurel, CLOE, Department for Biosciences, Royal Veterinary College - University of London, Zoologisches Institut, Universität Karlsruche, Institut für Genetik, Martin-Luther-Universität Halle Wittenberg (MLU), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Maynooth University Department of Biology Maynooth, National University of Ireland Maynooth (Maynooth University), School of Biological Sciences [Wellington, New Zealand], Victoria University of Wellington, Irish Centre for High-End Computing (ICHEC) (ICHE), Megazyme International, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Unidad Académica de Ciencias Biologicas, Laboratorio de Colecciones Biologicas y Sistematica Molecular, Universidad Autonoma de Zacatecas [Autonomous University of Zacatecas] (UAZ), Institute of Evolutionary Biology, CSIC-UPF, Edinburgh Genomics, School of Biological Sciences, University of Edinburgh, Institut fur Genetik, Volkswagen, German Research Foundation (DFG) SPP1819, European Research Council (ERC) ERC-2012-AdG 322790, Science Foundation Ireland RFP/EOB2506, Consejo Nacional de Ciencia y Tecnologia (CONACyT), Science Foundation Ireland 07/SK/B1236A, Biotechnology and Biological Sciences Research Council (BBSRC) BB/E/W/10964A01, NERC Natural Environment Research Council UKSBS PR18037, UAZ-2016-37096, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), National University of Ireland Maynooth (NUIM), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Universidad Autonoma de Zacatecas, Zacatecas, and Schiffer, Philipp H.
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Outcrossing, 02 engineering and technology, Biology, Genome, Article, transcriptomics, 03 medical and health sciences, Phylogenetics, Gene family, General, lcsh:Science, Transcriptomics, Cryptobiosis, Evolutionary Biology, Multidisciplinary, evolutionary biology, fungi, Parthenogenesis, 021001 nanoscience & nanotechnology, phylogenetics, 030104 developmental biology, Evolutionary biology, Horizontal gene transfer, lcsh:Q, Adaptation, 0210 nano-technology
Abstract: Summary Most animal species reproduce sexually and fully parthenogenetic lineages are usually short lived in evolution. Still, parthenogenesis may be advantageous as it avoids the cost of sex and permits colonization by single individuals. Panagrolaimid nematodes have colonized environments ranging from arid deserts to Arctic and Antarctic biomes. Many are obligatory meiotic parthenogens, and most have cryptobiotic abilities, being able to survive repeated cycles of complete desiccation and freezing. To identify systems that may contribute to these striking abilities, we sequenced and compared the genomes and transcriptomes of parthenogenetic and outcrossing panagrolaimid species, including cryptobionts and non-cryptobionts. The parthenogens are triploids, most likely originating through hybridization. Adaptation to cryptobiosis shaped the genomes of panagrolaimid nematodes and is associated with the expansion of gene families and signatures of selection on genes involved in cryptobiosis. All panagrolaimids have acquired genes through horizontal gene transfer, some of which are likely to contribute to cryptobiosis., Highlights • Parthenogenesis in Panagrolaimus nematodes arose once through a hybridization event • Parthenogenetic Panagrolaimus are triploid but retain meiosis after millions of years • Panagrolaimus can be used as a model system to study aspects of animal parthenogenesis • The genomes of Panagrolaimus nematodes are shaped by their adaptation to cryptobiosis, Evolutionary Biology; Phylogenetics; Transcriptomics
Published: 2019

18. Improvement of eukaryotic proteins prediction from soil metagenomes

Author: Georgios Koutsovoulos, Mathilde Clément, Etienne Danchin, Justine Lipuma, Corinne Rancurel, Marc Bailly-Bechet, and Carole Belliardo
Subjects: Annotation, Metagenomics, Computational biology, Biology, Shotgun metagenomics, Gene, Genome
Abstract: Background: During the last decades, shotgun metagenomics and metabarcoding have highlighted the diversity of microorganisms from environmental or host-associated samples. Most assembled metagenome public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs and metagenome-assembled genomes (MAGs). Consequently, eukaryotic contigs and MAGs, with intrinsically different gene features, are not optimally annotated, resulting in an incorrect representation of the eukaryotic component of biodiversity, despite their biological relevance. Results: Using an automated analysis pipeline, we have filtered 7.9 billion of contigs from 6,873 soil metagenomes in the IMG/M database of the Joint Genome Institute to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins. Of these, 5.6 million could be traced back to non-chimeric higher confidence eukaryotic contigs. Our pipeline improves eukaryotic proteins completeness, contiguity and quality. Moreover, the better quality of eukaryotic proteins combined with a more comprehensive assignment method improves the taxonomic annotation as well. Conclusions | Using public soil metagenomic data, we provide a dataset of eukaryotic soil proteins with improved completeness and quality as well as a more reliable taxonomic annotation. This unique resource is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.
Published: 2021

19. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga

Author: Karine Van Doninck, Richard Cordaux, Thomas Lenormand, Clément Gilbert, Karine Labadie, Lyam Baudry, Julie Virgo, Boris Hespeels, Djampa K. L. Kozlowski, Jitendra Narayan, Alessandro Derzelle, Marie Cariou, Antoine Limasset, Florence Gaudray, Bernard Hallet, Martial Marbouty, Etienne Danchin, Antoine Houtain, Rohan Arora, Matthieu Terwagne, Corinne Cruaud, Nadège Guiglielmoni, Jean-François Flot, Romain Koszul, Paul Simion, Emilien Nicolas, Marc Llirós, Université de Namur [Namur] (UNamur), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Collège Doctoral, Sorbonne Université (SU), Université libre de Bruxelles (ULB), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), 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), Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta - Girona Biomedical Research Institute (IDIBGI), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Louvain Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain = Catholic University of Louvain (UCL), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Interuniversity Institute of Bioinformatics in Brussels (IB2), Université libre de Bruxelles (ULB)-Vrije Universiteit Brussel (VUB), This project received funding from the Horizon 2020 research and innovation program under European Research Council (ERC) grant agreement 725998 (RHEA) and from BELSPO PRODEX for the ESA selected ILSRA-2014-0106 Project to K.V.D., from the Fédération Wallonie-Bruxelles via an 'Action de Recherche Concertée' (ARC) grant to K.V.D. and B.Ha., from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement 764840 to J.-F.F. (ITN IGNITE), from the Fédération Wallonie-Bruxelles via an Action de Recherche Concertée (ARC) grant to J.-F.F., from the European Research Council under the Horizon 2020 Program (ERC grant agreement 260822) and JPI-EC-AMR STARCS ANR-16-JPEC-0003-05 grant to R.K., and through funding by the French Government 'Investissement d’Avenir' program FRANCE GENOMIQUE (ANR-10-INBS-09). E.N. obtained an FSR UNamur fund. A.H., A.D., and R.A. are Research Fellows of the Fonds de la Recherche Scientifique—FNRS., ANR-16-JPEC-0003,STARCS,Selection and Transmission of Antimicrobial Resistance in Complex Systems(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), European Project: 764840,IGNITE, European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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, Sequence assembly, Rotifer, Evolution des espèces, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, Homologous chromosome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Océanographie biologique, Clade, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Biologie moléculaire, Chromosome, Adineta vaga, Genome, LOH, Adineta vaga, bdelloid rotifer, biology.organism_classification, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, chemistry, Génétique, cytogénétique, Systématique des espèces [zoologie], DNA, Recombination
Abstract: Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-term asexuality and DNA breakage on genome evolution. To this end, we present the first high-quality chromosome-level genome assemblies for the bdelloid Adineta vaga, composed of six pairs of homologous (diploid) chromosomes with a footprint of paleotetraploidy. The observed large-scale losses of heterozygosity are signatures of recombination between homologous chromosomes, either during mitotic DNA double-strand break repair or when resolving programmed DNA breaks during a modified meiosis. Dynamic subtelomeric regions harbor more structural diversity (e.g. chromosome rearrangements, transposable elements, and haplotypic divergence). Our results trigger the reappraisal of potential meiotic processes in bdelloid rotifers and help unravel the factors underlying their long-term asexual evolutionary success., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2021

20. The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5

Author: Rick E. Masonbrink, N. Zahid, Clement Pellegrin, U. Sonawala, Mark G. Sterken, Etienne Danchin, O. P. Kranse, Julia Holbein, Johannes Helder, C. Hiltl, J. J. M. van Steenbrugge, M. S. Hasan, Miroslaw Sobczak, Slawomir Janakowski, Tom R. Maier, Jose L. Lozano-Torres, Divykriti Chopra, Badou Mendy, Shahid Siddique, Peter Thorpe, Florian M. W. Grundler, Helen Beasley, O. Chitambo, Samer S. Habash, Tarek Hewezi, S. Eves-van den Akker, Esther Riemer, Georgios Koutsovoulos, Martijn Holterman, Eric Grenier, Thomas J. Baum, and Zoran S. Radakovic
Subjects: Transcriptome, Genetics, Nematode, biology, Host (biology), Horizontal gene transfer, Hologenome theory of evolution, biology.organism_classification, Heterodera schachtii, Genome, Gene
Abstract: Plant-parasitic nematodes are a major, and in some cases a dominant, threat to crop production in all agricultural systems. The relative scarcity of classical resistance genes highlights a pressing need to identify new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major stages of the interaction. This novel approach enabled the analysis of the hologenome of the infection site, to identify metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that the highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is critically important for parasitism. Knockout of either the plant-encoded or the now nematode-encoded steps in the pathway blocks parasitism. Our experiments establish a reference for cyst nematodes, use this platform to further our fundamental understanding of the evolution of plant-parasitism by nematodes, and show that understanding congruent differential expression of metabolic pathways represents a new way to find nematode susceptibility genes, and thereby, targets for future genome editing-mediated generation of nematode-resistant crops.
Published: 2021

21. Author Correction: Horizontal Gene Transfer of Pectinases from Bacteria Preceded the Diversification of Stick and Leaf Insects

Author: Etienne Danchin, David G. Heckel, Matan Shelomi, Sven Bradler, Xin Zhou, Yannick Pauchet, and Benjamin Wipfler
Subjects: Multidisciplinary, Bacteria, Gene Transfer, Horizontal, biology, Sequence Analysis, RNA, Science, Diversification (marketing strategy), biology.organism_classification, Neoptera, Gastrointestinal Microbiome, Evolution, Molecular, Polygalacturonase, Horizontal gene transfer, Botany, Medicine, Animals, Insect Proteins, Author Correction, Phylogeny
Abstract: Genes acquired by horizontal transfer are increasingly being found in animal genomes. Understanding their origin and evolution requires knowledge about the phylogenetic relationships from both source and recipient organisms. We used RNASeq data and respective assembled transcript libraries to trace the evolutionary history of polygalacturonase (pectinase) genes in stick insects (Phasmatodea). By mapping the distribution of pectinase genes on a Polyneoptera phylogeny, we identified the transfer of pectinase genes from known phasmatodean gut microbes into the genome of an early euphasmatodean ancestor that took place between 60 and 100 million years ago. This transfer preceded the rapid diversification of the suborder, enabling symbiont-free pectinase production that would increase the insects' digestive efficiency and reduce dependence on microbes. Bacteria-to-insect gene transfer was thought to be uncommon, however the increasing availability of large-scale genomic data may change this prevailing notion.
Published: 2021

22. Beyond social learning

Author: Pieter van den Berg, Guillaume Isabel, Thom Scott-Phillips, Edwin J. C. Van Leeuwen, Monica Tamariz, Alberto Acerbi, Christine A. Caldwell, Manvir Singh, Etienne Danchin, Maxime Derex, Lucas Molleman, Institute for Advanced Study in Toulouse (IAST), Brunel University London [Uxbridge], University of Stirling, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches sur la Cognition Animale - UMR5169 (CRCA), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Centre de Biologie Intégrative (CBI), University of Amsterdam [Amsterdam] (UvA), Central European University [Budapest, Hongrie] (CEU), Heriot-Watt University [Edinburgh] (HWU), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), University of Antwerp (UA), Royal Zoological Society of Antwerp (RZSA), Toulouse School of Economics (TSE-R), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-17-EURE-0010,CHESS,Toulouse Graduate School défis en économie et sciences sociales quantitatives(2017), Centre National de la Recherche Scientifique (CNRS), Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École des hautes études en sciences sociales (EHESS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), DSR-SCD-UT1C, Service Publications, and Toulouse Graduate School défis en économie et sciences sociales quantitatives - - CHESS2017 - ANR-17-EURE-0010 - EURE - VALID
Subjects: adaptation, cultural evolution, culture, cumulative culture, mechanism, social learning, Humans, Cultural Evolution, Social Learning, Big Five personality traits and culture, Affect (psychology), Biochemistry, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, [SCCO]Cognitive science, 0302 clinical medicine, Sociology, Sociocultural evolution, Adaptation (computer science), Biology, B- ECONOMIE ET FINANCE, 030304 developmental biology, [SHS.ANTHRO-SE] Humanities and Social Sciences/Social Anthropology and ethnology, 0303 health sciences, Agricultural and Biological Sciences(all), Mechanism (biology), Biochemistry, Genetics and Molecular Biology(all), [SCCO] Cognitive science, [SHS.ANTHRO-SE]Humanities and Social Sciences/Social Anthropology and ethnology, Social learning, Epistemology, Part II: Unravelling the Mechanisms Underlying Cultural Evolution, [SCCO.PSYC]Cognitive science/Psychology, Human medicine, General Agricultural and Biological Sciences, Explanatory power, 030217 neurology & neurosurgery, Theme (narrative), Genetics and Molecular Biology(all)
Abstract: One contribution of 15 to a theme issue ‘Foundations of cultural evolution’ compiled and edited by Eva Boon, Lucas Molleman, Pieter van den Berg and Franz J. Weissing. © 2021 The Author(s). Cultural evolution requires the social transmission of information. For this reason, scholars have emphasized social learning when explaining how and why culture evolves. Yet cultural evolution results from many mechanisms operating in concert. Here, we argue that the emphasis on social learning has distracted scholars from appreciating both the full range of mechanisms contributing to cultural evolution and how interactions among those mechanisms and other factors affect the output of cultural evolution. We examine understudied mechanisms and other factors and call for a more inclusive programme of investigation that probes multiple levels of the organization, spanning the neural, cognitive-behavioural and populational levels. To guide our discussion, we focus on factors involved in three core topics of cultural evolution: the emergence of culture, the emergence of cumulative cultural evolution and the design of cultural traits. Studying mechanisms across levels can add explanatory power while revealing gaps and misconceptions in our knowledge. ANR Institute for Advanced Study in Toulouse funding (grant ANR-17-EURE-0010 (Investissements d'Avenir program)); European Research Council (ERC) Consolidator Grant (No. 648841 RATCHETCOG). European Research Council, under the European Union's Seventh Framework Programme (FP'l/2007-2013)/ERC grant agreement no. 609819 (Somics project); European Union's Horizon 2020 Research and Innovation Programme (under Marie Sklodowska-Curie grant agreement number 748310).
Published: 2021

23. Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant‐parasitic nematode Meloidogyne incognita

Author: Mégane Karaulic, Laetitia Perfus-Barbeoch, Loris Pratx, Pierre Abad, Georgios Koutsovoulos, Etienne Danchin, Philippe Castagnone-Sereno, Marc Bailly-Bechet, Martine Da Rocha, Karine Mulet, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Plant Health and Environment INRA Division, French Government (National Research Agency, ANR)French National Research Agency (ANR) [392 ANR-13-JSV7-000], European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), and 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)
Subjects: 0106 biological sciences, 0301 basic medicine, DNA Copy Number Variations, [SDV]Life Sciences [q-bio], Asexual reproduction, Plant Roots, 010603 evolutionary biology, 01 natural sciences, Evolution, Molecular, gene copy number variations, 03 medical and health sciences, Reproduction, Asexual, Genetic variation, Genetics, Meloidogyne incognita, Animals, Tylenchoidea, experimental evolution, Copy-number variation, parthenogenesis, root-knot nematodes, Gene, Plant Physiological Phenomena, Ecology, Evolution, Behavior and Systematics, Plant Diseases, Experimental evolution, adaptive evolution, biology, Genomics, Plants, biology.organism_classification, Biological Evolution, 030104 developmental biology, Nematode, 13. Climate action, array comparative genomic hybridization, [SDE]Environmental Sciences, Adaptation
Abstract: International audience; Adaptation to changing environmental conditions represents a challenge to parthenogenetic organisms, and until now, how phenotypic variants are generated in clones in response to the selection pressure of their environment remains poorly known. The obligatory parthenogenetic root-knot nematode species Meloidogyne incognita has a worldwide distribution and is the most devastating plant-parasitic nematode. Despite its asexual reproduction, this species exhibits an unexpected capacity of adaptation to environmental constraints, for example, resistant hosts. Here, we used a genomewide comparative hybridization strategy to evaluate variations in gene copy numbers between genotypes of M. incognita resulting from two parallel experimental evolution assays on a susceptible vs. resistant host plant. We detected gene copy number variations (CNVs) associated with the ability of the nematodes to overcome resistance of the host plant, and this genetic variation may reflect an adaptive response to host resistance in this parthenogenetic species. The CNV distribution throughout the nematode genome is not random and suggests the occurrence of genomic regions more prone to undergo duplications and losses in response to the selection pressure of the host resistance. Furthermore, our analysis revealed an outstanding level of gene loss events in nematode genotypes that have overcome the resistance. Overall, our results support the view that gene loss could be a common class of adaptive genetic mechanism in response to a challenging new biotic environment in clonal animals.
Published: 2019

24. Response to Kalchhauser et al.: Inherited Gene Regulation Is not Enough to Understand Nongenetic Inheritance

Author: Benoit Pujol, Etienne Danchin, Pim Edelaar, Anne Charmantier, Russell Bonduriansky, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide [Sevilla] (UPO), School of Biological, Earth and Environmental Sciences [Sydney] (BEES), University of New South Wales [Sydney] (UNSW), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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 pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, Regulation of gene expression, Genetics, 0303 health sciences, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Biology, 010603 evolutionary biology, 01 natural sciences, Evolution, Molecular, 03 medical and health sciences, Inheritance (object-oriented programming), Gene Expression Regulation, Epigenetics, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: International audience
Published: 2021

25. A simple ATAC-seq protocol for population epigenetics

Author: Vicki A. Thomson, Olivier Rey, Sina Tönges, Patrice David, Christoph Grunau, David Duval, Cristian Chaparro, Jeremie Vidal-Dupiol, Aki Minoda, Mariana Gomes Lima, Emilien Luquet, Déborah Federico, Etienne Danchin, Dominique Joly, Silvain Pinaud, Fabien Aubret, Céline Cosseau, Ronaldo de Carvalho Augusto, Mamadou Dia Sow, Jean-François Allienne, Ranja Andriantsoa, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Cancer Research UK Cambridge Institute [Cambridge, Royaume-Uni] (CRUK), University of Cambridge [UK] (CAM), German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Équipe 1 - Biodiversité et Adaptation dans les Hydrosystèmes (BAH), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Station d'écologie théorique et expérimentale (SETE), Observatoire Midi-Pyrénées (OMP), Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), University of Adelaide, Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Instituto Oswaldo Cruz / Oswaldo Cruz Institute [Rio de Janeiro] (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratory for Cardiovascular Genomics and Informatics [Yokohama] (RIKEN IMS), RIKEN Center for Integrative Medical Sciences [Yokohama] (RIKEN IMS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN)-RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Station d’Ecologie Expérimentale du CNRS à Moulis (SEEM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université d'Orléans (UO), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 pour le Développement (IRD [France-Sud]), Évolution, génomes, comportement et écologie (EGCE), and Centre National de la Recherche Scientifique (CNRS)-IRD-Université Paris-Sud - Paris 11 (UP11)
Subjects: 0106 biological sciences, 0301 basic medicine, Euchromatin, [SDV]Life Sciences [q-bio], Population, Medicine (miscellaneous), ATAC-seq, Computational biology, Biology, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Epigenetics, education, Protocol (object-oriented programming), Transposase, Epigenomics, Protocol (science), education.field_of_study, epigenetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Articles, Schistosoma mansoni, Method Article, Chromatin, 030104 developmental biology, epigenomics, Daphnia pulex
Abstract: version 2; peer review: 2 approved; International audience; We describe here a protocol for the generation of sequence-ready libraries for population epigenomics studies, and the analysis of alignment results. We show that the protocol can be used to monitor chromatin structure changes in populations when exposed to environmental cues. The protocol is a streamlined version of the Assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) that provides a positive display of accessible, presumably euchromatic regions. The protocol is straightforward and can be used with small individuals such as daphnia and schistosome worms, and probably many other biological samples of comparable size (~10,000 cells), and it requires little molecular biology handling expertise.
Published: 2021

26. Recent Advances in Population Genomics of Plant-Parasitic Nematodes

Author: Etienne Danchin, Eric Grenier, Josselin Montarry, Georgios Koutsovoulos, Dave T Ste-Croix, Benjamin Mimee, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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 National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agriculture and Agri-Food [Ottawa] (AAFC), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 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), Université de Rennes (UR)-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), Agriculture and Agri-Food (AAFC), Université Nice Sophia Antipolis (1965 - 2019) (UNS), and 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
Subjects: 0106 biological sciences, 0301 basic medicine, Modes of reproduction, Nematoda, [SDV]Life Sciences [q-bio], Population genetics, Genomics, Plant Science, adaptation, Biology, evolutionary genetics, 01 natural sciences, Genome, DNA sequencing, cyst nematodes, Population genomics, 03 medical and health sciences, genomics, Animals, Parasites, root-knot nematodes, genome, Plant Diseases, 2. Zero hunger, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Human evolutionary genetics, food and beverages, population genetics, Plants, plant resistance, 030104 developmental biology, Evolutionary biology, Metagenomics, Adaptation, Agronomy and Crop Science, 010606 plant biology & botany
Abstract: International audience; Plant-parasitic nematodes are a costly burden of crop production. Ubiquitous in nature, phytoparasitic nematodes are associated with nearly every important agricultural crop and represent a significant constraint on global food security. Population genetics is a key discipline in plant nematology to understand aspects of the life strategies of these parasites, in particular their modes of reproduction, geographic origins, evolutionary histories, and dispersion abilities. Advances in high-throughput sequencing technologies have enabled a recent but active effort in genomic analyses of plant-parasitic nematodes. Such genomic approaches applied to multiple populations are providing new insights into the molecular and evolutionary processes that underpin the establishment of these nematodes and into a better understanding of the genetic and mechanistic basis of their pathogenicity and adaptation to their host plants. In this review, we attempt to update information about genome resources and genotyping techniques useful for nematologists who are thinking about initiating population genomics or genome sequencing projects. This review is intended also to foster the development of population genomics in plant-parasitic nematodes through highlighting recent publications that illustrate the potential for this approach to identify novel molecular markers or genes of interest and improve our knowledge of the genome variability, pathogenicity, and evolutionary potential of plant-parasitic nematodes.
Published: 2021

27. Chromatin structure changes in Daphnia populations upon exposure to environmental cues – or – The discovery of Wolterecks 'Matrix'

Author: Emilien Luquet, Silvain Pinaud, Fabien Aubret, Aki Minoda, Vicki A. Thomson, Etienne Danchin, Céline Cosseau, Patrice David, Dominique Joly, David Duval, Ranja Andriantsoa, Mariana Gomes Lima, Jean-François Allienne, Jeremie Vidal-Dupiol, Déborah Federico, Cristian Chaparro, Christoph Grunau, Ronaldo de Carvalho Augusto, Oliver Rey, Mamadou Dia Sow, Sina Tönges, Interactions Hôtes-Pathogènes-Environnements (IHPE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Institut National de la Recherche Agronomique (INRA)-Université d'Orléans (UO), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 pour le Développement (IRD [France-Sud]), University of Adelaide, Evolution, génomes, comportement et écologie (EGCE), Institut de Recherche pour le Développement (IRD)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratório de Malacologia [Rio de Janeiro], Instituto Oswaldo Cruz / Oswaldo Cruz Institute [Rio de Janeiro] (IOC), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, These experiments were done in the framework of the RTP 3E summer school 'Epigenetics for field ecologists' and received support from the CNRS., Interactions Hôtes-Pathogènes-Environnements [2015-...] (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Parasitologie fonctionnelle et évolutive [2003-2006] (PFE), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Ecologie et évolution des interactions [2011-2014] (2EI), Centre National de la Recherche Scientifique (CNRS), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université d'Orléans (UO)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, 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), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Phenotypic plasticity, biology, [SDV]Life Sciences [q-bio], fungi, ATAC-seq, ATAC-Seq, 010501 environmental sciences, Gene mutation, biology.organism_classification, 01 natural sciences, Daphnia pulex, Daphnia, Chromatin, 03 medical and health sciences, Reaction norm, Evolutionary biology, population epigenetics, norm of reaction, Epigenetics, Adaptation, 030304 developmental biology, 0105 earth and related environmental sciences
Abstract: Phenotypic plasticity is an important feature of biological systems that is likely to play a major role in the future adaptation of organisms to the ongoing global changes. It may allow an organism to produce alternative phenotypes in responses to environmental cues. Modifications in the phenotype can be reversible but are sometimes enduring and can even span over generations. The notion of phenotypic plasticity was conceptualized in the early 20thcentury by Richard Woltereck. He introduced the idea that the combined relations of a phenotypic character and all environmental gradients that influence on it can be defined as “norm of reaction”. Norms of reaction are specific to species and to lineages within species, and they are heritable. He postulated that reaction norms can progressively be shifted over generations depending on the environmental conditions. One of his biological models was the water-fleedaphnia. Woltereck proposed that enduring phenotypic modifications and gene mutations could have similar adaptive effects, and he postulated that their molecular bases would be different. Mutations occurred in genes, while enduring modifications were based on something he called theMatrix. He suggested that this matrix (i) was associated with the chromosomes, (ii) that it was heritable, (iii) it changed during development of the organisms, and (iv) that changes of the matrix could be simple chemical substitutions of an unknown, but probably polymeric molecule. We reasoned that the chromatin has all postulated features of this matrix and revisited Woltereck’s classical experiments withdaphnia. We developed a robust and rapid ATAC-seq technique that allows for analyzing chromatin of individual daphnia and show here (i) that this technique can be used with minimal expertise in molecular biology, and (ii) we used it to identify open chromatin structure in daphnia exposed to different environmental cues. Our result indicates that chromatin structure changes consistently in daphnia upon this exposure confirming Woltereck’s classical postulate.
Published: 2020

28. Characterization of raffinose metabolism genes uncovers a wild Arachis galactinol synthase conferring tolerance to abiotic stresses

Author: Brenda N Porto, Ana Cristina Miranda Brasileiro, A. L. Lacerda, Thais Nicolini Oliveira, Etienne Danchin, C. C. Vinson, Iracyara Sampaio, Thomas C. R. Williams, Patricia Messenberg Guimaraes, Ana Paula Zotta Mota, Brazilian Agricultural Research Corporation (Embrapa), Universidade de Brasilia [Brasília] (UnB), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 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), Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA), INCT PlantStress Biotech 465480/2014-4, FAPDF (Distrito Federal Research Foundation) 0193.001565/2017, Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ), Science without Boarders CNPq program, CHRISTINA C. VINSON, UNB, ANA P. Z. MOTA, BRENDA N. PORTO, THAIS N. OLIVEIRA, IRACYARA SAMPAIO, UNB, ANA L. LACERDA, ETIENNE G. J. DANCHIN, UNIVERSITÉ CÔTE D'AZUR, FRANCE, PATRICIA MESSEMBERG GUIMARAES, Cenargen, THOMAS C. R. WILLIAMS, UNB, and ANA CRISTINA MIRANDA BRASILEIRO, Cenargen.
Subjects: 0106 biological sciences, 0301 basic medicine, Arachis, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], Arabidopsis, lcsh:Medicine, Oligosaccharides, Disaccharides, 01 natural sciences, Article, Arachis duranensis, 03 medical and health sciences, chemistry.chemical_compound, Raffinose, Gene Expression Regulation, Plant, Stress, Physiological, lcsh:Science, Plant Proteins, 2. Zero hunger, Genetics, Abiotic component, [SDV.GEN]Life Sciences [q-bio]/Genetics, Multidisciplinary, beta-Fructofuranosidase, biology, Abiotic stress, Transgenic plants, lcsh:R, Fabaceae, 15. Life on land, Galactosyltransferases, Plants, Genetically Modified, biology.organism_classification, Gene expression profiling, Droughts, 030104 developmental biology, chemistry, RFOs, lcsh:Q, 010606 plant biology & botany
Abstract: Raffinose family oligosaccharides (RFOs) are implicated in plant regulatory mechanisms of abiotic stresses tolerance and, despite their antinutritional proprieties in grain legumes, little information is available about the enzymes involved in RFO metabolism in Fabaceae species. In the present study, the systematic survey of legume proteins belonging to five key enzymes involved in the metabolism of RFOs (galactinol synthase, raffinose synthase, stachyose synthase, alpha-galactosidase, and beta-fructofuranosidase) identified 28 coding-genes in Arachis duranensis and 31 in A. ipaënsis. Their phylogenetic relationships, gene structures, protein domains, and chromosome distribution patterns were also determined. Based on the expression profiling of these genes under water deficit treatments, a galactinol synthase candidate gene (AdGolS3) was identified in A. duranensis. Transgenic Arabidopsis plants overexpressing AdGolS3 exhibited increased levels of raffinose and reduced stress symptoms under drought, osmotic, and salt stresses. Metabolite and expression profiling suggested that AdGolS3 overexpression was associated with fewer metabolic perturbations under drought stress, together with better protection against oxidative damage. Overall, this study enabled the identification of a promising GolS candidate gene for metabolic engineering of sugars to improve abiotic stress tolerance in crops, whilst also contributing to the understanding of RFO metabolism in legume species.
Published: 2020

29. Author Correction: Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode

Author: Sebastian Kiewnick, Etienne Danchin, Christian H. Ahrens, Juerg E. Frey, Marine Poullet, Djampa K. L. Kozlowski, Cristina Martin-Jimenez, Georgios Koutsovoulos, Erika Sallet, Laetitia Perfus-Barbeoch, Abdelnaser Elashry, and Martine Da Rocha
Subjects: Statistics and Probability, Sequence assembly, Computational biology, Parthenogenesis, Library and Information Sciences, Biology, biology.organism_classification, Computer Science Applications, Education, Meloidogyne enterolobii, Annotation, Root-knot nematode, lcsh:Q, Statistics, Probability and Uncertainty, lcsh:Science, Information Systems
Abstract: A Correction to this paper has been published: https://doi.org/10.1038/s41597-020-00747-0.
Published: 2020

30. Comparative Genomics Reveals Novel Target Genes Towards Specific Control of Plant-Parasitic Nematodes

Author: Priscila Grynberg, Corinne Rancurel, José Dijair Antonino, Robert Neil Gerard Miller, Etienne Danchin, Marcos Mota do Carmo Costa, Roberto C. Togawa, Leticia Dias de Freitas, Patricia Messenberg Guimaraes, Ana Cristina Miranda Brasileiro, Maria Fatima Grossi-de-Sa, Embrapa Genetic Resources and Biotechnology, University of Bras ılia, Brazilian Agricultural Research Corporation (Embrapa), Universidade de Brasilia [Brasília] (UnB), Universidade Federal Rural de Pernambuco (UFRPE), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (... - 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), Universidade Católica de Brasília (UCB), University of Brasilia [Brazil] (UnB), CNPq PVE Science without Borders Program 401541/2014-2, Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES) 88887.310583/2018-00, Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ) 465480/2014-4, INCT PlantStress Biotech (FAPDF project) 193.001.265/2017, Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES) 001, and Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ)
Subjects: 0106 biological sciences, 0301 basic medicine, lcsh:QH426-470, Gene Transfer, Horizontal, Nematoda, de novo gene birth, [SDV]Life Sciences [q-bio], Genomics, comparative genomics, Computational biology, 01 natural sciences, Genome, Article, Host-Parasite Interactions, 03 medical and health sciences, Phylogenomics, Genetics, Meloidogyne incognita, Animals, anatomy_morphology, Computer Simulation, Tylenchoidea, Gene, Phylogeny, Genetics (clinical), Plant Diseases, 2. Zero hunger, Comparative genomics, Genome, Helminth, biology, Effector, plant-parasitic nematodes, phylogenomics, Helminth Proteins, Plants, biology.organism_classification, horizontal gene transfers, parasite-specific genes, lcsh:Genetics, Gene Ontology, 030104 developmental biology, Nematode, Gene Expression Regulation, pest control, 010606 plant biology & botany
Abstract: Plant-parasitic nematodes cause expressive annual yield losses to worldwide agricultural production. Most cultivated plants have no known resistance against nematodes and the few bearing a resistance gene can be overcome by certain species. The chemical methods that have been deployed to control nematodes were largely banned from use due to their poor specificity and high toxicity. Hence, there is an urgent need for the development of cleaner and more specific control methods. Recent advances in nematode genomics, including in phytoparasitic species, provide an unprecedented opportunity to identify genes and functions specific to these pests. Using phylogenomics, we compared 61 nematode genomes, including 16 for plant-parasitic species and identified more than 24,000 protein families specific to these parasites. In the genome of Meloidogyne incognita, one of the most devastating plant parasites, we found ca. 10,000 proteins with orthologs restricted only to phytoparasitic species and no further homology in protein databases. Among these phytoparasites-specific proteins, ca. 1,000 shared the same properties as known secreted effectors involved in essential parasitic functions. Of those, 68 were novel and showed strong expression during the endophytic phase of the nematode life cycle, based on both RNA-seq and RT-qPCR analyses. Besides effector candidates, transcription-related and neuro-perception functions were enriched in phytoparasites-specific proteins, revealing interesting targets for nematode control methods. This phylogenomics analysis, constitutes an unprecedented resource for the further understanding of the genetic basis of nematode adaptation to phytoparasitism and for the development of more efficient control methods.
Published: 2020

31. Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode

Author: Sebastian Kiewnick, Martine Da Rocha, Abdelnaser Elashry, Juerg E. Frey, Djampa K. L. Kozlowski, Cristina Martin-Jimenez, Etienne Danchin, Georgios Koutsovoulos, Christian H. Ahrens, Laetitia Perfus-Barbeoch, Erika Sallet, Marine Poullet, 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), Strube Research GmbH & Co. KG, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroscope, Julius Kühn-Institut (JKI), ANR-13-JSV7-0006,ASEXEVOL,Un génome fait de multiples copies divergentes permet-il à un animal parasite de plantes d'évoluer en l'absence de reproduction sexuée ?(2013), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), and Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: 0106 biological sciences, Transposable element, Statistics and Probability, Data Descriptor, [SDV]Life Sciences [q-bio], Meloidogyne Enterolobii, Sequence assembly, Biology, Library and Information Sciences, Genome informatics, 01 natural sciences, Genome, Education, 03 medical and health sciences, Animals, Root-knot nematode, Tylenchoidea, lcsh:Science, Author Correction, Gene, Genome size, Plant Diseases, 030304 developmental biology, 2. Zero hunger, Genome, Helminth, 0303 health sciences, Contig, Comparative genomics, Root-knot Nematodes, fungi, food and beverages, biology.organism_classification, Computer Science Applications, Europe, Meloidogyne enterolobii, Evolutionary biology, lcsh:Q, Pathogens, Statistics, Probability and Uncertainty, 010606 plant biology & botany, Information Systems
Abstract: Root-knot nematodes (genus Meloidogyne) are plant parasites causing huge economic loss in the agricultural industry and affecting severely numerous developing countries. Control methods against these plant pests are sparse, the preferred one being the deployment of plant cultivars bearing resistance genes against Meloidogyne species. However, M. enterolobii is not controlled by the resistance genes deployed in the crop plants cultivated in Europe. The recent identification of this species in Europe is thus a major concern. Here, we sequenced the genome of M. enterolobii using short and long-read technologies. The genome assembly spans 240 Mbp with contig N50 size of 143 kbp, enabling high-quality annotations of 59,773 coding genes, 4,068 non-coding genes, and 10,944 transposable elements (spanning 8.7% of the genome). We validated the genome size by flow cytometry and the structure, quality and completeness by bioinformatics metrics. This ensemble of resources will fuel future projects aiming at pinpointing the genome singularities, the origin, diversity, and adaptive potential of this emerging plant pest., Measurement(s) genome • sequence_assembly • sequence feature annotation Technology Type(s) DNA sequencing assay • sequence assembly process • sequence annotation Sample Characteristic - Organism Meloidogyne enterolobii Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12410363
Published: 2020
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32. Intraspecific difference among herbivore lineages and their host-plant specialization drive the strength of trophic cascades

Author: Arnaud Sentis, Alexandra Magro, Jean-Louis Hemptinne, Etienne Danchin, Raphael Bertram, Benoit Pujol, Jean-Christophe Simon, Nathalie Dardenne, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-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), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), ANR‐10‐LABX‐25‐01, Agence Nationale de la Recherche, Campus France, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-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 National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, Food Chain, Lineage (evolution), [SDV]Life Sciences [q-bio], Nutritional Status, Biology, 010603 evolutionary biology, 01 natural sciences, Intraspecific competition, Predation, 03 medical and health sciences, Genetic variation, Specialization (functional), host-plant adaptation, Trophic cascade, Ecology, Evolution, Behavior and Systematics, indirect effects, 030304 developmental biology, Trophic level, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, Herbivore, tri-trophic interactions, Ecology, herbivory, 010604 marine biology & hydrobiology, Evo-to-eco, Plants, Biological Evolution, Ecological network, [SDE]Environmental Sciences, genetic variation, Trait
Abstract: Trophic cascades—the indirect effect of predators on non-adjacent lower trophic levels—are important drivers of the structure and dynamics of ecological communities. However, the influence of intraspecific trait variation on the strength of trophic cascade remains largely unexplored, which limits our understanding of the mechanisms underlying ecological networks. Here we experimentally investigated how intraspecific difference among herbivore lineages specialized on different host plants influences the strength of trophic cascade in a terrestrial tritrophic system. We found that the occurrence and strength of the trophic cascade are strongly influenced by herbivores’ lineage and host-plant specialization but are not associated with density-dependent effects mediated by the growth rate of herbivore populations. Our findings stress the importance of intraspecific heterogeneities and evolutionary specialization as drivers of the strength of trophic cascades and underline that intraspecific variation should not be overlooked to decipher the joint influence of evolutionary and ecological factors on the functioning of multi-trophic interactions.
Published: 2020

33. Homologous chromosomes in asexual rotifer Adineta vaga suggest automixis

Author: Martial Marbouty, Benjamin Noel, Bernard Hallet, Paul Simion, Patrick Wincker, Djampa K. L. Kozlowski, Romain Koszul, Etienne Danchin, Jitendra Narayan, Antoine Houtain, Antoine Limasset, Marie Cariou, Emilien Nicolas, Florence Gaudray, Lyam Baudry, Julie Virgo, Karine Van Doninck, Alessandro Derzelle, Jean-François Flot, Matthieu Terwagne, and Nadège Guiglielmoni
Subjects: Genetics, Genome evolution, Meiosis, Homologous chromosome, Chromosome, Parthenogenesis, Biology, Genome, Synteny, Reference genome
Abstract: The several hundreds of species of bdelloid rotifers are notorious because they represent an ancient clade comprising only asexual lineages1. Moreover, most bdelloid species have the ability to withstand complete desiccation and high doses of ionizing radiation, being able to repair their DNA after massive genome breakage2. To better understand the impact of long-term asexuality and DNA breakage on genome evolution, a telomere-to-tolemere reference genome assembly of a bdelloid species is critical3, 4. Here we present the first, high quality chromosome-scale genome assembly for the bdelloid A. vaga validated using three complementary assembly procedures combined with chromosome conformation capture (Hi-C) data. The different assemblies reveal the same genome architecture and using fluorescent in situ hybridization (FISH), we demonstrate that the A. vaga genome is composed of six pairs of homologous chromosomes, compatible with meiosis. Moreover, the synteny between homoeologous (or ohnologous) chromosomes is also preserved, confirming their paleotetraploidy. The diploid genome structure of A. vaga and the presence of very long homozygous tracts show that recombination between homologous chromosomes occurs in this ancient asexual scandal, either during DSB repair or during meiotic pairing. These homozygosity tracts are mainly observed towards the chromosome ends in the clonal A. vaga suggesting signatures of a parthenogenetic mode of reproduction equivalent to central fusion automixis, in which homologous chromosomes are not segregated during the meiotic division.
Published: 2020

34. Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita

Author: Djampa K. L. Kozlowski, Rahim Hassanaly-Goulamhoussen, Etienne Danchin, Georgios Koutsovoulos, Marc Bailly-Bechet, and Martine Da Rocha
Subjects: Transposable element, Population genomics, Polyploid, biology, Evolutionary biology, Meloidogyne incognita, food and beverages, Single-nucleotide polymorphism, biology.organism_classification, Genome, Terra incognita, Reference genome
Abstract: Despite reproducing without sexual recombination, the root-knot nematode Meloidogyne incognita is adaptive and versatile. Indeed, this species displays a global distribution, is able to parasitize a large range of plants and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability without sex remain poorly known and only low variation at the single nucleotide polymorphism level have been observed so far across different geographical isolates with distinct ranges of compatible hosts. Hence, other mechanisms than the accumulation of point mutations are probably involved in the genomic dynamics and plasticity necessary for adaptability. Transposable elements (TEs), by their repetitive nature and mobility, can passively and actively impact the genome dynamics. This is particularly expected in polyploid hybrid genomes such as the one of M. incognita. Here, we have annotated the TE content of M. incognita, analyzed the statistical properties of this TE content, and used population genomics approach to estimate the mobility of these TEs across 12 geographical isolates, presenting phenotypic variations. The TE content is more abundant in DNA transposons and the distribution of TE copies identity to their consensuses sequence suggests they have been at least recently active. We have identified loci in the genome where the frequencies of presence of a TE showed variations across the different isolates. Compared to the M. incognita reference genome, we detected the insertion of some TEs either within genic regions or in the upstream regulatory regions. These predicted TEs insertions might thus have a functional impact. We validated by PCR the insertion of some of these TEs, confirming TE movements probably play a role in the genome plasticity with possible functional impacts.
Published: 2020

35. Genome sequence of the root-knot nematode Meloidogyne luci

Author: Saša Širca, Polona Strajnar, David H. Lunt, Barbara Gerič Stare, Cristian Riccio, Georgios Koutsovoulos, Gregor Urek, Mark Blaxter, Etienne Danchin, and Nik Susič
Subjects: Whole genome sequencing, PacBio, education.field_of_study, Genome, Contig, Population, Sequence assembly, Genomics, Agricultural pest, Biology, biology.organism_classification, Root-knot nematode, Illumina, Meloidogyne luci, lcsh:Biology (General), Genus, Botany, education, lcsh:QH301-705.5
Abstract: Root-knot nematodes from the genus Meloidogyne are polyphagous plant endoparasites and agricultural pests of global importance. Here, we report the high-quality genome sequence of Meloidogyne luci population SI-Smartno V13. The resulting genome assembly of M. luci SI-Smartno V13 consists of 327 contigs, with an N50 contig length of 1,711,905 bp and a total assembly length of 209.16 Mb. Root-knot nematodes from the genus Meloidogyne are polyphagous plant endoparasites and agricultural pests of global importance. Here, we report the high-quality genome sequence of Meloidogyne luci population SI-Smartno V13. The resulting genome assembly of M. luci SI-Smartno V13 consists of 327 contigs, with an N50 contig length of 1,711,905 bp and a total assembly length of 209.16 Mb.
Published: 2020

36. Epigenetics in ecology and evolution

Author: Anthony Herrel, Dominique Joly, Etienne Danchin, Evolutionary Morphology of Vertebrates, Ghent University [Belgium] (UGENT), Centre de Lutte contre le Cancer, CHU Clermont-Ferrand-Centre Jean Perrin, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University [Belgium] (UGENT), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER-UNICANCER-CHU Clermont-Ferrand, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Universiteit Gent = Ghent University (UGENT), Mécanismes Adaptatifs et Evolution (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Phenotypic plasticity, Ecology (disciplines), [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, Inheritance (genetic algorithm), Context (language use), Epigenome, Biology, 010603 evolutionary biology, 01 natural sciences, Evolutionary biology, Evolutionary ecology, Adaptation, Evolutionary dynamics, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 010606 plant biology & botany
Abstract: The discovery of the multidimensional nature of the inherited information carried by the epigenome and the characterization of its intra‐ and intergenerational dynamics have profoundly changed our understanding of the functioning of biological organisms and the origins of phenotypic diversity. This has raised considerable interest in the study of epigenetics which is emerging as a ‘missing link’ between environmental and phenotypic variation. Recent discoveries have provided important insights into the mechanisms of phenotypic plasticity, inheritance and adaptation; key concepts at the crossroads of individual‐centred approaches (that mostly study proximate mechanisms); and supra‐individual ones (that mostly study ultimate processes). In this context, epigenetics emerges as a major source of inquiry for the study of ecological and evolutionary dynamics. This special feature provides an overview of the role of epigenetics in ecology and evolution.
Published: 2019

37. Different phenotypic plastic responses to predators observed among aphid lineages specialized on different host plants

Author: Arnaud Sentis, Jean-Christophe Simon, Alexandra Magro, Ines Louit, Benoit Pujol, Gaël Le Trionnaire, Jean-Louis Hemptinne, Raphaël Bertram, Etienne Danchin, Nathalie Dardenne, Felipe Ramon-Portugal, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Evolution biologique, Université de Provence - Aix-Marseille 1-EA 3781, ANR-10-LABX-25-01, Agence Nationale de la Recherche, PCOFUND-GA-2013-609102, Seventh Framework Programme, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, 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), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Sentis, Arnaud, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE)
Subjects: 0301 basic medicine, reproductive isolation, [SDV]Life Sciences [q-bio], lcsh:Medicine, Evolutionary ecology, Predation, 0302 clinical medicine, morphology, Medicago, Wings, Animal, lcsh:Science, ComputingMilieux_MISCELLANEOUS, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Aphid, Multidisciplinary, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Food webs, food and beverages, mediated plasticity, Reproductive isolation, Plants, Biological Evolution, Phenotype, genetic-variation, Evolutionary developmental biology, races, Plastics, Medicago sativa, life-history, pea aphid, evolution, behavior, resistance, Zoology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Article, Intraspecific competition, Host-Parasite Interactions, 03 medical and health sciences, Genetic variation, Animals, Herbivory, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], lcsh:R, Phenotypic trait, 15. Life on land, biology.organism_classification, Acyrthosiphon pisum, 030104 developmental biology, Aphids, Predatory Behavior, lcsh:Q, 030217 neurology & neurosurgery, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: [Departement_IRSTEA]Eaux [ADD1_IRSTEA]Dynamique et fonctionnement des écosystèmes; International audience; The role of intraspecific variation in the magnitude and direction of plastic responses in ecology and evolution is increasingly recognized. However, the factors underlying intraspecific variation in plastic responses remain largely unexplored, particularly for the hypothesis that the herbivores' phenotypic response to predators might vary amongst lineages associated with different host plants. Here, we tested whether plant-specialized lineages of the pea aphid, Acyrthosiphon pisum, differed in their transgenerational phenotypic response to ladybird predators (i.e., the asexual production of winged offspring by wingless mothers). In a full factorial laboratory experiment, we found that six aphid clonal lineages each specialized either on alfalfa or clover significantly differed in their transgenerational phenotypic response to predators. Some lineages produced an increased number of winged aphids in predator presence while others did not respond. Aphid lineages specialized on alfalfa had stronger phenotypic responses to predators than those specialized on clover. Although we tested only six aphid lineages from two biotypes, our results imply that intraspecific variation in prey phenotypic response of herbivores to predators differs amongst lineages specialized on different host plants. Our findings therefore raise the question of the influence of plant specialization in shaping herbivore phenotypic responses, and highlight the need to consider multi-trophic interactions to understand the causes and consequences of intraspecific variation in complex phenotypic traits.
Published: 2019

38. Mate-copying for a costly variant in Drosophila melanogaster females

Author: Sabine Nöbel, Guillaume Isabel, and Etienne Danchin
Subjects: 0106 biological sciences, 0301 basic medicine, Copying, biology, Genetic variants, biology.organism_classification, Social learning, 010603 evolutionary biology, 01 natural sciences, Phenotype, 03 medical and health sciences, 030104 developmental biology, Evolutionary biology, Animal Science and Zoology, Drosophila melanogaster, Ecology, Evolution, Behavior and Systematics
Abstract: Mate-copying is a form of social learning in which witnessing sexual interactions between conspecifics biases an observer female's future mate-choice. We show in the fruit fly that females of either the Curly-wing (Cy) or the wild-type (WT) phenotype, after observing another female preferring to copulate with a fitness-lowering Cy male over a WT male, increased their preference for the usually nonpreferred Cy phenotype. Thus, mate-copying also exists for costly variants in invertebrates.
Published: 2018

39. Effects of a sex ratio gradient on female mate-copying and choosiness in Drosophila melanogaster

Author: Etienne Danchin, Magdalena Monier, Guillaume Isabel, and Sabine Nöbel
Subjects: 0106 biological sciences, 0301 basic medicine, biology, media_common.quotation_subject, fungi, Behavioral pattern, biology.organism_classification, Affect (psychology), 010603 evolutionary biology, 01 natural sciences, Courtship, 03 medical and health sciences, 030104 developmental biology, 5. Gender equality, Mate choice, Animal Science and Zoology, Drosophila melanogaster, Mating, Drosophila, Sex ratio, Demography, media_common
Abstract: In many sexually reproducing species, individuals can gather information about potential mates by observing their mating success. This behavioral pattern, that we call mate-copying, was reported in the fruit fly Drosophila melanogaster where females choosing between 2 males of contrasting phenotypes can build a preference for males of the phenotype they previously saw being chosen by a demonstrator female. As sex ratio is known to affect mate choice, our goal was to test whether mate-copying is also affected by encountered sex ratios. Thus, we created a gradient of sex ratio during demonstrations of mate-copying experiments by changing the number of females observing from a central arena 6 simultaneous demonstrations unfolding in 6 peripheral compartments of a hexagonal device. We also tested whether the sex ratio experienced by females during demonstrations affected their choosiness (male courtship duration and double courtship rate) in subsequent mate-choice tests. Experimental male:female sex ratio during demonstrations did not affect mate-copying indices, but positively affected the proportion of both males courting the female during mate-choice tests, as well as male courtship duration, the latter potentially explaining the former relationship. As expected, the sex ratio affected female choosiness positively, and Drosophila females seem to have evolved a mate-copying ability independently of sex ratio, and a capacity to adapt their choosiness to male availability. This suggests that, as in many animal species, individuals, especially females, can adapt their mate choice depending on the current sex ratio.
Published: 2018

40. Targeted transcriptomics reveals signatures of large-scale independent origins and concerted regulation of effector genes in Radopholus similis

Author: Clement Pellegrin, Etienne Danchin, Thomas R. Maier, Lev G. Nemchinov, Sebastian Eves-van den Akker, Catherine Wram, Thomas J. Baum, Georgios Koutsovoulos, Cedar Hesse, Paulo Vieira, Jonathan Shao, Inga A. Zasada, Tracie K. Matsumoto, Roxana Y. Myers, Vieira, Paulo [0000-0001-5627-2628], Myers, Roxana Y [0000-0002-7465-7895], Hesse, Cedar [0000-0002-1006-0491], Koutsovoulos, Georgios D [0000-0003-3406-3715], Zasada, Inga [0000-0001-6603-3073], Danchin, Etienne GJ [0000-0003-4146-5608], Baum, Thomas J [0000-0001-9241-3141], Eves-van den Akker, Sebastian [0000-0002-8833-9679], Nemchinov, Lev G [0000-0003-0314-8150], Apollo - University of Cambridge Repository, and Eves-Van Den Akker, Sebastian [0000-0002-8833-9679]
Subjects: Nematoda, Plant Science, Biochemistry, Transcriptome, Medical Conditions, Carrots, Vegetables, Radopholus similis, Post-Translational Modification, Biology (General), Nematode Infections, Flowering Plants, Phylogeny, Effector, Eukaryota, Genomics, Helminth Proteins, Plants, Horizontal gene transfer, Neofunctionalization, Signal Peptides, Research Article, Nicotiana, Tylenchida, QH301-705.5, Immunology, Biology, Microbiology, Protein Domains, Virology, Tobacco, Parasitic Diseases, Genetics, Animals, Molecular Biology, Gene, Plant Diseases, Medicine and health sciences, Biology and life sciences, Organisms, Proteins, Plant Pathology, RC581-607, biology.organism_classification, Invertebrates, Nematode, Gene Expression Regulation, Evolutionary biology, Parasitology, Immunologic diseases. Allergy, Zoology
Abstract: The burrowing nematode, Radopholus similis, is an economically important plant-parasitic nematode that inflicts damage and yield loss to a wide range of crops. This migratory endoparasite is widely distributed in warmer regions and causes extensive destruction to the root systems of important food crops (e.g., citrus, banana). Despite the economic importance of this nematode, little is known about the repertoire of effectors owned by this species. Here we combined spatially and temporally resolved next-generation sequencing datasets of R. similis to select a list of candidates for the identification of effector genes for this species. We confirmed spatial expression of transcripts of 30 new candidate effectors within the esophageal glands of R. similis by in situ hybridization, revealing a large number of pioneer genes specific to this nematode. We identify a gland promoter motif specifically associated with the subventral glands (named Rs-SUG box), a putative hallmark of spatial and concerted regulation of these effectors. Nematode transcriptome analyses confirmed the expression of these effectors during the interaction with the host, with a large number of pioneer genes being especially abundant. Our data revealed that R. similis holds a diverse and emergent repertoire of effectors, which has been shaped by various evolutionary events, including neofunctionalization, horizontal gene transfer, and possibly by de novo gene birth. In addition, we also report the first GH62 gene so far discovered for any metazoan and putatively acquired by lateral gene transfer from a bacterial donor. Considering the economic damage caused by R. similis, this information provides valuable data to elucidate the mode of parasitism of this nematode., Author summary Radopholus similis is considered to be among the top 10 most damaging plant-parasitic nematodes world-wide. The molecular dialogue established by plant-parasitic nematodes and the host plant is driven by secreted nematode proteins, also known as effectors. Here we use targeted transcriptomics to predict and validate the most comprehensive set of effectors for this plant-parasitic nematode. Contrary to long-held assumptions that migratory nematodes are less specialized plant-parasitic nematodes, we showed that the repertoire of effectors of this migratory nematode is largely complex and novel. Among the 30 new effector genes identified, 19 were pioneer genes without a priori putative function or annotation but highly expressed during plant interaction. The identification of a promoter motif element for a significant set of these effectors suggest a concerted regulation of these genes by the nematode. The increase knowledge of the effector repertoire of this economic important species not only contributes to the understanding of the mechanisms of parasitism employed by migratory nematodes, but will also allow the development of effector gene targeted strategies to control this nematode.
Published: 2021

41. Kestrels rely on two different types of social information from conspecifics when choosing breeding habitats

Author: Etienne Danchin, Jesús Miguel Avilés Regodón, Nadia Silva, and María Deseada Parejo Mora
Subjects: Ecology, Reproductive success, biology, Context (language use), biology.organism_classification, Falco tinnunculus, Emigration, Geography, Habitat, Plumage, Social information, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm)
Abstract: Parejo, D., Silva, N., Danchin, E., Aviles, J.M. 2017. Kestrels rely on two different types of social information from conspecifics when choosing breeding habitats. Ecosistemas 26(3): 39-47. Doi.: 10.7818/ECOS.2017.26-3.06 Breeding habitat selection is strongly influenced by social information, which is that extracted from the behaviour and performance of other individuals. Also, signals shaped by selection to convey information may be used by unintended receivers as a particular form of social information that has been neglected in a breeding habitat selection context so far. Here, we first tested experimentally whether Eurasian kestrels (Falco tinnunculus) rely on social information provided by conspecifics’ performance by studying the impact of patch scale manipulations of the local reproductive success of conspecifics on their habitat selection during two consecutive years. Second, we provide correlative evidence for the use of plumage coloration of conspecifics as a potential source of social information in the same context of breeding habitat choice in the species. For this purpose, we collected information on individual plumage colouration during one year and analysed its relationship with the habitat choices of individuals in the following year. Our results show that Eurasian kestrels rely on conspecific breeding performance during their emigration decisions, and might rely on female plumage colouration as a signal of resident females’ quality for emigration and immigration decisions. That is, both sources of information, conspecific performance and signals indicating quality, may be used in habitat selection decisions by this species
Published: 2017

42. Écologie comportementale

Author: Étienne Danchin, Luc-Alain Giraldeau, Étienne Danchin, and Luc-Alain Giraldeau
Subjects: Phenotype, Ecophysiology, Animal behavior
Abstract: L'écologie comportementale est née de la nécessité de bien comprendre la façon dont fonctionne l'évolution pour produire l'incroyable diversité des formes du vivant. Cet ouvrage, rédigé par une vingtaine de spécialistes, sous la direction de Etienne Danchin, Luc-Alain Giraldeau et Frank Cézilly, présente une initiation complète et intégrée du comportement animal. Il est organisé autour des grandes décisions que l'individu doit prendre au cours de sa vie. Les deux derniers chapitres sont consacrés aux applications de l'écologie comportementale : élaboration de stratégies pour la conservation de la biodiversité et comparaison avec les comportements humains. Des questions de réflexion complètent le cours et en fin d'ouvrage, un glossaire bilingue de 260 entrées et un index très complet permettent d'aller rapidement à l'essentiel. Ont également contribué à cet ouvrage : Thierry Boulinier, Michel Chapuisat, Jean Clobert, Michèle de Fraipont, Alfred Dufty, Régis Ferrière, Jean-François Legalliard, Mylène Mariette, Anders P. Moller, Gabriele Sorci, Marc Théry.
Published: 2021

43. First evidence for a significant effect of the regression to the mean fallacy in mate copying: a comment on Davies et al

Author: Guillaume Isabel, Etienne Danchin, Arnaud Pocheville, Sabine Nöbel, and Institute for Advanced Study in Toulouse (IAST)
Subjects: 0106 biological sciences, Fallacy, 0303 health sciences, Copying, Biology, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Regression toward the mean, Statistics, Animal Science and Zoology, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: National audience
Published: 2020

44. Response to Comment on 'Cultural flies: Conformist social learning in fruitflies predicts long-lasting mate-choice traditions'

Author: Sabine Nöbel, Guillaume Isabel, Arnaud Pocheville, Etienne Danchin, Institute for Advanced Study in Toulouse (IAST), DSR-SCD-UT1C, Service Publications, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches sur la Cognition Animale - UMR5169 (CRCA), Institut des sciences du cerveau de Toulouse. (ISCT), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre de Recherches sur la Cognition Animale (CRCA), Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut des sciences du cerveau de Toulouse. (ISCT), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J)-CHU Toulouse [Toulouse]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Pocheville, Arnaud, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Long lasting, media_common.quotation_subject, 010603 evolutionary biology, 01 natural sciences, Conformity, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Animals, Learning, 0501 psychology and cognitive sciences, 050102 behavioral science & comparative psychology, Social Behavior, [SHS.ECO] Humanities and Social Sciences/Economics and Finance, ComputingMilieux_MISCELLANEOUS, media_common, Conformist, Multidisciplinary, Diptera, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 05 social sciences, Social learning, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Social Learning, Mate choice, Psychology, Social psychology
Abstract: National audience; Thornquist and Crickmore claim that systematic experimental error may explain the results of Danchin and colleagues. Their claim rests on mistakes in their analyses, for which we provide corrections. We reassert that conformity in fruitflies predicts long-lasting mate-preference traditions.
Published: 2019

45. Behavioural avoidance of sperm ageing depends on genetic similarity of mates in a monogamous seabird

Author: Richard H. Wagner, Etienne Danchin, Scott A. Hatch, Hervé Mulard, Pierrick Blanchard, Fabrice Helfenstein, Joël White, Maxime Pineaux, Sarah Leclaire, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Evolution biologique, Université de Provence - Aix-Marseille 1-EA 3781, United States Geological Survey (USGS), Institute of Biology [Switzerland], Université de Neuchâtel (UNINE), Ecologie et Neuro-Ethologie Sensorielles (ENES), Université Jean Monnet [Saint-Étienne] (UJM), Laboratoire Ecologie et évolution, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Sensory Neuro-Ethology (ENES), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and École normale supérieure - Paris (ENS-PSL)
Subjects: 0106 biological sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, [SDV]Life Sciences [q-bio], Biology, 010603 evolutionary biology, 01 natural sciences, Sperm, 03 medical and health sciences, Genetic similarity, Evolutionary biology, Ageing, biology.animal, Seabird, reproductive and urinary physiology, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Inbreeding, i.e. the mating of genetically related individuals, can lead to reduced fitness and is considered to be a major selective force of mate choice. Although inbreeding avoidance has been found in numerous taxa, individuals may face constraints when pairing, leading to mating with suboptimal partners. In such circumstances, individuals that are able to avoid factors exacerbating detrimental effects of inbreeding should be favoured. Using the socially and genetically monogamous black-legged kittiwake (Rissa tridactyla), we explored whether the detrimental effects of inbreeding are exacerbated by sperm ageing (i.e. the post-meiotic senescence of sperm cells, mainly occurring within the female tracts after copulation), and whether they can be mitigated by behavioural tactics. First, by experimentally manipulating the age of the fertilizing sperm, we found that hatching failure due to sperm ageing increased with higher genetic similarity between mates. We then investigated whether more genetically similar pairs exhibited mating behaviours that prevent fertilization by old sperm. The more genetically similar mates were, the less likely they were to copulate early in the reproductive season and the more females performed post-copulatory sperm ejections. By flexibly adapting their behaviour in response to within-pair genetic similarity, kittiwakes may avoid exacerbation of inbreeding costs due to sperm ageing.
Published: 2019

46. Sex and hatching order modulate the association between MHC-II diversity and fitness in early-life stages of a wild seabird

Author: Sarah Leclaire, Etienne Danchin, David Duneau, Maxime Pineaux, Thomas Merkling, Scott A. Hatch, Pierrick Blanchard, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Avian clutch size, Male, animal structures, Rissa tridactyla, Zoology, Major histocompatibility complex, 010603 evolutionary biology, 01 natural sciences, Major Histocompatibility Complex, 03 medical and health sciences, Charadriiformes, Immune system, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Genetics, Animals, Parasites, Selection, Genetic, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Alleles, biology, Hatching, Histocompatibility Antigens Class II, Genetic Variation, Heterozygote advantage, biology.organism_classification, 030104 developmental biology, embryonic structures, Kittiwake, biology.protein, Female, human activities, Diversity (business)
Abstract: Genes of the major histocompatibility complex (MHC) play a pivotal role in parasite resistance, and their allelic diversity has been associated with fitness variations in several taxa. However, studies report inconsistencies in the direction of this association, with either positive, quadratic or no association being described. These discrepancies may arise because the fitness costs and benefits of MHC diversity differ among individuals depending on their exposure and immune responses to parasites. Here, we investigated in black-legged kittiwake (Rissa tridactyla) chicks whether associations between MHC class-II diversity and fitness vary with sex and hatching order. MHC-II diversity was positively associated with growth and tick clearance in female chicks, but not in male chicks. Our data also revealed a positive association between MHC-II diversity and survival in second-hatched female chicks (two eggs being the typical clutch size). These findings may result from condition-dependent parasite infections differentially impacting sexes in relation to hatching order. We thus suggest that it may be important to account for individual heterogeneities in traits that potentially exert selective pressures on MHC diversity in order to properly predict MHC-fitness associations.
Published: 2019

47. Offspring sex-ratio and environmental conditions in a seabird with sex-specific rearing costs: a long-term experimental approach

Author: Scott A. Hatch, Sarah Leclaire, Thomas Merkling, Pierrick Blanchard, Etienne Danchin, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, United States Geological Survey (USGS), Evolution biologique, Université de Provence - Aix-Marseille 1-EA 3781, Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Rissa tridactyla, Offspring, [SDV]Life Sciences [q-bio], Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, 030104 developmental biology, Animal ecology, Kittiwake, Regime shift, Reproductive value, Ecology, Evolution, Behavior and Systematics, Sex allocation, Sex ratio, ComputingMilieux_MISCELLANEOUS, Demography
Abstract: Sex allocation studies among birds and mammals are notoriously inconsistent with theoretical predictions. One explanation is the difficulty of collecting data on costs and benefits of sex-ratio adjustments, which prevents the investigation of underlying assumptions. Some predictions may thus have been tested in species where they should not have been expected. Here, we focus on the “cost of reproduction hypothesis”, which states that parents with low investment capacity should avoid producing the most expensive sex to minimise the decrease in their residual reproductive value. In the black-legged kittiwake (Rissa tridactyla), sons are energetically more expensive than daughters. Using 10 years of data (1172 chicks from 790 broods) from a long-term feeding experiment, we predicted a stronger decrease in the probability of producing a son with deteriorating environmental conditions among Control than among supplementally Fed parents. To test this prediction, we used three proxies of environmental conditions and a recent sliding window approach. We found no support for our prediction. Hence, we investigated between-year sex-ratio variation in relation to feeding status to detect a response to an unmeasured environmental variable. There was no interaction between year and feeding status, nor any effect of feeding status itself. However, the probability of producing a male increased with time, which could be a response to an oceanic regime shift that occurred around our colony, but that our proxies failed to capture. Our study further highlights the difficulty of explaining sex-ratio variation in long-lived species with complex life-histories where multiple selective pressures can occur simultaneously.
Published: 2019

48. Cross-Kingdom Analysis of Diversity, Evolutionary History, and Site Selection within the Eukaryotic Macrophage Migration Inhibitory Factor Superfamily

Author: Etienne Danchin, Harald Keller, C Michelet, Christine Coustau, Maëlle Jaouannet, Karl-Heinz Kogel, Ralph Panstruga, Jürgen Bernhagen, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Ludwig-Maximilians-Universität München (LMU), Rheinisch-Westfälische Technische Hochschule Aachen (RWTH), Justus-Liebig-Universität Gießen (JLU), French National Research Agency (ANR) ANR-16-CE92-0014-01, DFG Ko 1208/26-1, DFG PA 861/15-1, French National Research Agency (ANR), German Research Foundation (DFG), French National Research Agency (ANR) ANR-11-LABX-0028-0, German Research Foundation (DFG) SFB1123/A3 SyNergy EXC1010, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-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), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH), Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), ANR-16-CE92-0014,X-KINGDOM-MIF,Analyse comparative de la fonction des 'Macrophage Migration Inhibitory Factor' (MIF) dans les règnes animaux et végétaux.(2016), and Coustau, Christine
Subjects: 0301 basic medicine, lcsh:QH426-470, Ecology (disciplines), animal diseases, Virulence, Biology, [SDV.IMM.II]Life Sciences [q-bio]/Immunology/Innate immunity, Article, Evolution, Molecular, 03 medical and health sciences, Negative selection, eukaryotes, ddc:570, Genetics, Animals, Humans, macrophage migration inhibitory factor, host-parasite interactions, innate immunity, phylogenetic reconstructions, Amino Acid Sequence, Macrophage Migration-Inhibitory Factors, Gene, Phylogeny, Genetics (clinical), Innate immune system, Base Sequence, 030102 biochemistry & molecular biology, Eukaryota, SUPERFAMILY, Protein superfamily, lcsh:Genetics, 030104 developmental biology, Evolutionary biology, Macrophage migration inhibitory factor
Abstract: Genes 10(10), E740 (2019). doi:10.3390/genes10100740 special issue: "Invertebrate Immunity", Published by MDPI, Basel
Published: 2019

49. Red coloration varies with dietary carotenoid access and nutritional condition in kittiwakes

Author: Scott A. Hatch, Pierrick Blanchard, Maxime Pineaux, Sarah Leclaire, Vincent Bourret, Etienne Danchin, Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut for Searbird Research and Conservation, Institut d'écologie et des sciences de l'environnement de Paris (IEES), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UPVM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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 pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Evolution biologique, Université de Provence - Aix-Marseille 1-EA 3781, and United States Geological Survey (USGS)
Subjects: Male, 0106 biological sciences, Physiology, Zeaxanthin, [SDV]Life Sciences [q-bio], Foraging, Color, Nutritional Status, Zoology, Xanthophylls, Aquatic Science, Biology, 010603 evolutionary biology, 01 natural sciences, Predation, Charadriiformes, 03 medical and health sciences, chemistry.chemical_compound, Astaxanthin, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animals, Bare part, 14. Life underwater, Molecular Biology, Carotenoid, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Gull, Pigmentation, Diet composition, Capelin, Ornaments, biology.organism_classification, Animal Feed, Diet, Ketocarotenoid, chemistry, Insect Science, Dietary Supplements, Animal Science and Zoology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: International audience; Carotenoid-based ornaments are common signaling features in animals. Although the mechanisms that link color-based signals to individual condition is key to understanding the evolution and function of these ornaments, they are most often poorly known. Several hypotheses have been posited. They include: (i) the role of foraging abilities on carotenoid acquisition and thereby carotenoid-based ornaments, and (ii) the role of internal processes linked to individual quality on the allocation and conversion of carotenoids in integuments. Here, we tested the influence of dietary carotenoid access versus internal process on gape coloration in black-legged kittiwakes (Rissa tridactyla). This seabird displays a vibrant red gape, whose coloration varies with individual quality in males and is due to the deposition of red ketocarotenoids, such as astaxanthin. We decreased hydroxycarotenoid and ketocarotenoid levels in plasma, but increased efficiency in internal processes linked to nutritional condition, by supplementing breeding males with capelin, a natural energy-rich fish prey. We found that, despite having lower carotenoid levels in plasma, supplemented birds developed redder coloration than control birds, but only in the year when dietary levels of astaxanthin in the natural diet were low. In contrast, in the astaxanthin-rich year, supplemented males had a less-red gape than unsupplemented birds. These results suggest that inter-individual differences in internal processes may be sufficient to maintain the honesty of gape coloration under conditions of low dietary astaxanthin levels. Nonetheless, when inter-individual variations in dietary astaxanthin levels are elevated (such as in the crustacean-rich year), carotenoid access seems a more limiting factor to the expression of gape coloration than internal processes. Therefore, our study revealed a complex mechanism of gape color production in kittiwakes, and suggests that the main factor maintaining the condition dependency of this ornaments may vary with environmental conditions and diet composition.
Published: 2019

50. Population genomics supports clonal reproduction and multiple independent gains and losses of parasitic abilities in the most devastating nematode pest

Author: Laurent Duret, Philippe Castagnone-Sereno, Etienne Danchin, Andressa Cristina Zamboni Machado, Djampa K. L. Kozlowski, Regina M. D. G. Carneiro, Erika V.S. Albuquerque, Georgios Koutsovoulos, Eder Marques, Marc Bailly-Bechet, Marie-Jeanne Arguel, Institut Sophia Agrobiotech (ISA), Institut National de la Recherche Agronomique (INRA)-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), Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), IPMC, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Université Côte d'Azur (UCA), 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), Université de Lyon, Área de Proteção de Plantas, Instituto Agronômico do Parana (IAPAR), Empresa Brasileira de Pesquisa Agropecuaria, Institut National de la Recherche Agronomique SPE 2016, French National Research Agency (ANR) ANR-13-JSV7-0006-ASEXEVOL, Consorcio Pesquisa Cafe, European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), UMR 5558 Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique (CNRS), Instituto Agronômico do Parana, Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), 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)-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)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), PPGFS/Fac. Agronomia, Universidade Federal de Pelotas = Federal University of Pelotas (UFPel), COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), and Danchin, Etienne
Subjects: 0106 biological sciences, 0301 basic medicine, Linkage disequilibrium, population genomics, [SDV]Life Sciences [q-bio], clonal evolution, lcsh:Evolution, 010603 evolutionary biology, 01 natural sciences, Genome, Population genomics, 03 medical and health sciences, host races, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Meloidogyne incognita, lcsh:QH359-425, agricultural pest, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Phylogenetic tree, biology, Host (biology), [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], food and beverages, Original Articles, biology.organism_classification, 030104 developmental biology, parallel adaptation, Evolutionary biology, Original Article, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], General Agricultural and Biological Sciences, Terra incognita, Reference genome
Abstract: International audience; The root‐knot nematodes are the most devastating worms to worldwide agriculture with Meloidogyne incognita being the most widely distributed and damaging species. This parasitic and ecological success seems surprising given its supposed obligatory clonal reproduction. Clonal reproduction has been suspected based on cytological observations but, so far, never confirmed by population genomics data. As a species, M. incognita is highly polyphagous with thousands of host plants. However, different M. incognita isolates present distinct and overlapping patterns of host compatibilities. Historically, four “host races” had been defined as a function of ranges of compat‐ible and incompatible plants. In this study, we used population genomics to assess whether (a) reproduction is actually clonal in this species, (b) the host races follow an underlying phylogenetic signal or, rather represent multiple independent transitions, and (c) how genome variations associate with other important biological traits such as the affected crops and geographical distribution. We sequenced the genomes of 11 M. incognita isolates across Brazil that covered the four host races in replicates. By aligning the genomic reads of these isolates to the M. incognita reference genome assembly, we identified point variations. Analysis of linkage disequilibrium and 4‐gametes test showed no evidence for recombination, corroborating the clonal re‐production of M. incognita. The few point variations between the isolates showed no significant association with the host races, the geographical origin of the samples, or the crop on which they have been collected. Addition of isolates from other locations around the world confirmed this lack of underlying phylogenetic signal. This suggests multiple gains and losses of parasitic abilities and adaptations to different environ‐ments account for the broad host spectrum and wide geographical distribution of M. incognita and thus to its economic impact. pact. This surprising adaptability without sex poses both evolutionary and agro‐economic challenges.
Published: 2019

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