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2. Sex-related differences in aging rate are associated with sex chromosome system in amphibians

Author

Cayuela, Hugo, Lemaître, Jean-François, Léna, Jean-Paul, Ronget, Victor, Martínez-Solano, Iñigo, Muths, Erin, Pilliod, David S., Schmidt, Benedikt R., Sánchez-Montes, Gregorio, Gutiérrez-Rodríguez, Jorge, Pyke, Graham, Grossenbacher, Kurt, Lenzi, Omar, Bosch, Jaime, Beard, Karen H., Woolbright, Lawrence L., Lambert, Brad A., Green, David M., Jreidini, Nathalie, Garwood, Justin M., Fisher, Robert N., Matthews, Kathleen, Dudgeon, David, Lau, Anthony, Speybroeck, Jeroen, Homan, Rebecca, Jehle, Robert, Başkale, Eyup, Mori, Emiliano, Arntzen, Jan W., Joly, Pierre, Stiles, Rochelle M., Lannoo, Michael J., Maerz, John C., Lowe, Winsor H., Valenzuela-Sánchez, Andrés, Christiansen, Ditte G., Angelini, Claudio, Thirion, Jean-Marc, Merilä, Juha, Colli, Guarino R., Vasconcellos, Mariana M., Boas, Taissa C. V., da C. Arantes, Ísis, Levionnois, Pauline, Reinke, Beth A., Vieira, Cristina, Marais, Gabriel A. B., Gaillard, Jean-Michel, and Miller, David A. W.

Published
2022

8. The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Author

Badouin, Hélène, Velt, Amandine, Gindraud, François, Flutre, Timothée, Dumas, Vincent, Vautrin, Sonia, Marande, William, Corbi, Jonathan, Sallet, Erika, Ganofsky, Jérémy, Santoni, Sylvain, Guyot, Dominique, Ricciardelli, Eugenia, Jepsen, Kristen, Käfer, Jos, Berges, Hélène, Duchêne, Eric, Picard, Franck, Hugueney, Philippe, Tavares, Raquel, Bacilieri, Roberto, Rustenholz, Camille, and Marais, Gabriel A. B.

Published
2020
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11. Amphioxus functional genomics and the origins of vertebrate gene regulation

Author

Marlétaz, Ferdinand, Firbas, Panos N., Maeso, Ignacio, Tena, Juan J., Bogdanovic, Ozren, Perry, Malcolm, Wyatt, Christopher D. R., de la Calle-Mustienes, Elisa, Bertrand, Stephanie, Burguera, Demian, Acemel, Rafael D., van Heeringen, Simon J., Naranjo, Silvia, Herrera-Ubeda, Carlos, Skvortsova, Ksenia, Jimenez-Gancedo, Sandra, Aldea, Daniel, Marquez, Yamile, Buono, Lorena, Kozmikova, Iryna, Permanyer, Jon, Louis, Alexandra, Albuixech-Crespo, Beatriz, Le Petillon, Yann, Leon, Anthony, Subirana, Lucie, Balwierz, Piotr J., Duckett, Paul Edward, Farahani, Ensieh, Aury, Jean-Marc, Mangenot, Sophie, Wincker, Patrick, Albalat, Ricard, Benito-Gutiérrez, Èlia, Cañestro, Cristian, Castro, Filipe, D’Aniello, Salvatore, Ferrier, David E. K., Huang, Shengfeng, Laudet, Vincent, Marais, Gabriel A. B., Pontarotti, Pierre, Schubert, Michael, Seitz, Hervé, Somorjai, Ildiko, Takahashi, Tokiharu, Mirabeau, Olivier, Xu, Anlong, Yu, Jr-Kai, Carninci, Piero, Martinez-Morales, Juan Ramon, Crollius, Hugues Roest, Kozmik, Zbynek, Weirauch, Matthew T., Garcia-Fernàndez, Jordi, Lister, Ryan, Lenhard, Boris, Holland, Peter W. H., Escriva, Hector, Gómez-Skarmeta, Jose Luis, and Irimia, Manuel

Published
2018
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13. TheSilene latifoliagenome and its giant Y chromosome

Author

Moraga, Carol, primary, Branco, Catarina, additional, Rougemont, Quentin, additional, Veltsos, Paris, additional, Jedlička, Pavel, additional, Muyle, Aline, additional, Hanique, Melissa, additional, Tannier, Eric, additional, Liu, Xiaodong, additional, Mendoza-Galindo, Eddy, additional, Lemaitre, Claire, additional, Fields, Peter D., additional, Cruaud, Corinne, additional, Labadie, Karine, additional, Belser, Caroline, additional, Briolay, Jerome, additional, Santoni, Sylvain, additional, Cegan, Radim, additional, Linheiro, Raquel, additional, de la Vega, Ricardo C. Rodríguez, additional, Adam, Gabriele, additional, Filali, Adil El, additional, Mossion, Vinciane, additional, Boualem, Adnane, additional, Tavares, Raquel, additional, Chebbi, Amine, additional, Cordaux, Richard, additional, Fruchard, Cécile, additional, Prentout, Djivan, additional, Velt, Amandine, additional, Spataro, Bruno, additional, Delmotte, Stephane, additional, Weingartner, Laura, additional, Toegelová, Helena, additional, Tulpová, Zuzana, additional, Cápal, Petr, additional, Šimková, Hana, additional, Štorchová, Helena, additional, Krüger, Manuela, additional, Abeyawardana, Oushadee A. J., additional, Taylor, Douglas R., additional, Olson, Matthew S., additional, Sloan, Daniel B., additional, Karrenberg, Sophie, additional, Delph, Lynda F., additional, Charlesworth, Deborah, additional, Giraud, Tatiana, additional, Bendahmane, Abdelhafid, additional, Genova, Alex Di, additional, Madoui, Amin, additional, Hobza, Roman, additional, and Marais, Gabriel A. B., additional

Published
2023
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14. Transposable element expression with variation in sex chromosome number supports a toxic Y effect on human longevity

Author

Teoli, Jordan, primary, Fablet, Marie, additional, Bardel, Claire, additional, Necsulea, Anamaria, additional, Labalme, Audrey, additional, Lejeune, Hervé, additional, Lemaitre, Jean-François, additional, Gueyffier, François, additional, Sanlaville, Damien, additional, Vieira, Cristina, additional, Marais, Gabriel AB, additional, and Plotton, Ingrid, additional

Published
2023
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15. Self-compassion and savouring buffer the impact of the first year of the COVID-19 on PhD students' mental health

Author

Paucsik, Marine, Leys, Christophe, Marais, Gabriel, Baeyens, Céline, Shankland, Rebecca RS, Paucsik, Marine, Leys, Christophe, Marais, Gabriel, Baeyens, Céline, and Shankland, Rebecca RS

Abstract

Doctoral students face many challenges that were reinforced by COVID-19-related lockdowns. We assessed this impact over 1 year on doctoral students' depression, anxiety, stress, well-being, and doctoral engagement. We also investigated the potential protective role of self-compassion and savouring on mental health, well-being, and doctoral engagement. A total of 134 PhD students from several French universities responded to the three-time points of this longitudinal study. The results showed a significant increase in depression, anxiety and stress and a significant decrease in well-being and doctoral engagement during the first year of the pandemic. Self-compassion and savouring predicted lower levels of depression, anxiety, and stress, and higher levels of well-being over time. Savouring alone predicted higher doctoral engagement over time. This study reveals the significant impact of the pandemic year on the mental health of doctoral students, and the relevance of self-compassion and savouring as psychological resources to cope with adversity., SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2023

19. Lockdown and PhD Student

Author

Paucsik, Marine, Leys, Christophe, Marais, Gabriel, Celine, Baeyens, and Shankland, Rebecca

Abstract

Mental health of PhD Student during COVID-19

Published
2022
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20. Impact of lockdown on the mental health of French PhD students

Author

Paucsik, Marine, Shankland, Rebecca, Celine, Baeyens, and Marais, Gabriel

Subjects
FOS: Psychology, lockdown, Clinical Psychology, stress, Phd Student, education, depression, Psychology, Social and Behavioral Sciences, mental health
Abstract

As the lockdown continues, PhD students represent a population at risk of developing symptoms of stress, anxiety and depression, as well as decreased motivation for thesis work. Indeed, the thesis experience is already considered difficult as it is characterized by constant peer pressure, frequent evaluations, low status, high workload, high pressure to publish, and financial difficulties (Schmidt & Umans, 2014). COVID-19-related lockdown could reinforce these issues and impact the quality of life and work of doctoral students. Some find themselves isolated, others in poor working conditions, and others see their research interrupted. This is one of the reasons why the Minister of Higher Education, Frédérique Vidal, has just authorized the organizations and institutions that host doctoral students to extend the duration of their thesis as well as their doctoral contract. In this context, because of the duration of the lockdown, which is likely to be extended for at least some doctoral students, it is useful to identify protective factors in order to encourage the support and development of these factors. The aim of this brief survey is therefore to identify mental health as symptoms of stress, anxiety, depression, degree of mental well-being, motivation and engagement in thesis work, and protective factors like self-compassion (inverse of negative repetitive self-criticism) and savouring (capacity to savour past, present and future satisfying events).

Published
2022
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25. Sex-related differences in aging rate areassociated with sex chromosome system inamphibians

Author

Swiss National Science Foundation, Cayuela, Hugo, Lemaître, Jean-François, Léna, Jean-Paul, Ronget, Víctor, Martínez-Solano, Íñigo, Muths, Erin, Pilliod, David S., Schmidt, Benedikt R., Sánchez-Montes, Gregorio, Gutiérrez-Rodríguez, Jorge, Pyke, Graham, Grossenbacher, Kurt, Lenzi, Omar, Bosch, Jaime, Beard, Karen H., Woolbright, Lawrence L, Lambert, Brad A., Green, David M., Jreidini, Nathalie, Garwood, Justin M., Fisher, Robert N., Matthews, Kathleen, Dudgeon, David, Lau, Anthony, Speybroeck, Jeroen, Homan, Rebecca, Jehle, Robert, Baskale, Eyup, Mori, Emiliano, Arntzen, Jan W., Joly, Pierre, Stile, Rochelle M., Lannoo, Michael J., Maerz, John C., Lowe, Winsor H., Valenzuela-Sánchez, Andrés, Christiansen, Ditte G., Angelini, Claudio, Thirion, Jean-Marc, Merilä, Juha, Colli, Guarino R., Vasconcellos, Mariana M., Boas, Taissa C.V., Arantes, Ísis da C., Levionnois, Pauline, Reinke, Beth A., Vieira, Cristina, Marais, Gabriel A.B., Gaillard, Jean-Michel, Miller, David A.W., Swiss National Science Foundation, Cayuela, Hugo, Lemaître, Jean-François, Léna, Jean-Paul, Ronget, Víctor, Martínez-Solano, Íñigo, Muths, Erin, Pilliod, David S., Schmidt, Benedikt R., Sánchez-Montes, Gregorio, Gutiérrez-Rodríguez, Jorge, Pyke, Graham, Grossenbacher, Kurt, Lenzi, Omar, Bosch, Jaime, Beard, Karen H., Woolbright, Lawrence L, Lambert, Brad A., Green, David M., Jreidini, Nathalie, Garwood, Justin M., Fisher, Robert N., Matthews, Kathleen, Dudgeon, David, Lau, Anthony, Speybroeck, Jeroen, Homan, Rebecca, Jehle, Robert, Baskale, Eyup, Mori, Emiliano, Arntzen, Jan W., Joly, Pierre, Stile, Rochelle M., Lannoo, Michael J., Maerz, John C., Lowe, Winsor H., Valenzuela-Sánchez, Andrés, Christiansen, Ditte G., Angelini, Claudio, Thirion, Jean-Marc, Merilä, Juha, Colli, Guarino R., Vasconcellos, Mariana M., Boas, Taissa C.V., Arantes, Ísis da C., Levionnois, Pauline, Reinke, Beth A., Vieira, Cristina, Marais, Gabriel A.B., Gaillard, Jean-Michel, and Miller, David A.W.

Abstract

Sex-related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determinationsystems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due toan apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females)systems. Taking advantage of a unique collection of capture–recapture datasets in amphibians, a vertebrate group where XY andZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sexdifferences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and notlifespan) differ between XY and ZW systems. Sex-specific variation in aging rates was moderate within each system, but agingrates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome systemon sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleteriousmutations on the X/Z chromosome (the “unguarded X/Z effect”) or repeat-rich Y/W chromosome (the “toxic Y/W effect”) couldaccelerate aging in the heterogametic sex in some vertebrate clades.

Published
2022

27. Supplementary Material from Dosage compensation evolution in plants: theories, controversies and mechanisms

Author

Muyle, Aline, Marais, Gabriel A. B., Ba��ovsk��, V��clav, Hobza, Roman, and Lenormand, Thomas

Subjects
food and beverages
Abstract

In a minority of flowering plants, separate sexes are genetically determined by sex chromosomes. The Y chromosome has a non-recombining region that degenerates, causing a reduced expression of Y genes. In some species, the lower Y expression is accompanied by dosage compensation (DC), a mechanism that re-equalizes male and female expression and/or brings XY male expression back to its ancestral level. Here, we review work on DC in plants, which started as early as the late 60 s with cytological approaches. The use of transcriptomics fired a controversy as to whether DC existed in plants. Further work revealed that various plants exhibit partial DC, including a few species with young and homomorphic sex chromosomes. We are starting to understand the mechanisms responsible for DC in some plants, but in most species, we lack the data to differentiate between global and gene-by-gene DC. Also, it is unknown why some species evolve many dosage compensated genes while others do not. Finally, the forces that drive DC evolution remain mysterious, both in plants and animals. We review the multiple evolutionary theories that have been proposed to explain DC patterns in eukaryotes with XY or ZW sex chromosomes.This article is part of the theme issue ���Sex determination and sex chromosome evolution in land plants���.

Published
2022
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37. A derived ZW chromosome system in Amborella trichopoda , representing the sister lineage to all other extant flowering plants

Author

Käfer, Jos, primary, Bewick, Adam, additional, Andres‐Robin, Amélie, additional, Lapetoule, Garance, additional, Harkess, Alex, additional, Caïus, José, additional, Fogliani, Bruno, additional, Gâteblé, Gildas, additional, Ralph, Paula, additional, dePamphilis, Claude W., additional, Picard, Franck, additional, Scutt, Charlie, additional, Marais, Gabriel A. B., additional, and Leebens‐Mack, James, additional

Published
2021
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38. Studying genetic antagonisms as drivers of genome evolution

Author

Joron, Mathieu, Shearn, Rylan, Wright, Alison, Mousset, Sylvain, Régis, Corinne, Penel, Simon, Lemaitre, Jean- François, Douay, Guillaume, Crouau-Roy, Brigitte, Lecompte, Emilie, Marais, Gabriel, 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), 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, 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)

Subjects
0106 biological sciences, 0303 health sciences, Genome evolution, Philosophy, [SDV]Life Sciences [q-bio], Pseudoautosomal region, General Medicine, 010603 evolutionary biology, 01 natural sciences, Genealogy, 03 medical and health sciences, Wright, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

A recommendation of: Rylan Shearn, Alison E. Wright, Sylvain Mousset, Corinne Regis, Simon Penel, Jean-Francois Lemaitre, Guillaume Douay, Brigitte Crouau-Roy, Emilie Lecompte, Gabriel A.B. Marais Evolutionary stasis of the pseudoautosomal boundary in strepsirrhine primates 10.1101/445072

Published
2020
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39. Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene

Author

Muyle, Aline, Martin, Helene, Zemp, Niklaus, Mollion, Maeva, Gallina, Sophie, Tavares, Raquel, Silva, Alexandre, Bataillon, Thomas, Widmer, Alex, Glemin, Sylvain, Touzet, Pascal, Marais, Gabriel A. B., Muyle, Aline, Martin, Helene, Zemp, Niklaus, Mollion, Maeva, Gallina, Sophie, Tavares, Raquel, Silva, Alexandre, Bataillon, Thomas, Widmer, Alex, Glemin, Sylvain, Touzet, Pascal, and Marais, Gabriel A. B.

Abstract

About 15,000 angiosperm species (similar to 6%) have separate sexes, a phenomenon known as dioecy. Why dioecious taxa are so rare is still an open question. Early work reported lower species richness in dioecious compared with nondioecious sister clades, raising the hypothesis that dioecy may be an evolutionary dead-end. This hypothesis has been recently challenged by macroevolutionary analyses that detected no or even positive effect of dioecy on diversification. However, the possible genetic consequences of dioecy at the population level, which could drive the long-term fate of dioecious lineages, have not been tested so far. Here, we used a population genomics approach in the Silene genus to look for possible effects of dioecy, especially for potential evidence of evolutionary handicaps of dioecy underlying the dead-end hypothesis. We collected individual-based RNA-seq data from several populations in 13 closely related species with different sexual systems: seven dioecious, three hermaphroditic, and three gynodioecious species. We show that dioecy is associated with increased genetic diversity, as well as higher selection efficacy both against deleterious mutations and for beneficial mutations. The results hold after controlling for phylogenetic inertia, differences in species census population sizes and geographic ranges. We conclude that dioecious Silene species neither show signs of increased mutational load nor genetic evidence for extinction risk. We discuss these observations in the light of the possible demographic differences between dioecious and self-compatible hermaphroditic species and how this could be related to alternatives to the dead-end hypothesis to explain the rarity of dioecy.

Published
2021
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41. Intron size and exon evolution in drosophila

Author

Marais, Gabriel, Nouvellet, Pierre, Keightley, Peter D., and Charlesworth, Brian

Subjects
Evolution -- Research, Drosophila -- Research, Drosophila -- Genetic aspects, Biological sciences
Abstract

We have found a negative correlation between evolutionary rate at the protein level (as measured by [d.sub.N]) and intron size in Drosophila. Although such a relation is expected if introns reduce Hill-Robertson interference within genes, it seems more likely to be explained by the higher abundance of cis-regulatory elements in introns (especially first introns) in genes under strong selective constraints.

Published
2005

42. Patterns of selection against transposons inferred from the distribution of Tc1, Tc3 and Tc5 insertions in the mut-7 line of the nematode Caenorhabditis elegans

Author

Rizzon, Carene, Martin, Edwidge, Marais, Gabriel, Duret, Laurent, Segalat, Laurent, and Biemont, Christian

Subjects
Caenorhabditis elegans -- Genetic aspects, Caenorhabditis elegans -- Research, Transposons -- Research, Biological sciences
Abstract

To identify the factors (selective or mutational) that affect the distribution of transposable elements (TEs) within a genome, it is necessary to compare the pattern of newly arising element insertions to the pattern of element insertions that have been fixed in a population. To do this, we analyzed the distribution of recent mutant insertions of the Tc1, Tc3, and Tc5 elements in a mut-7 background of the nematode Caenorhabditis elegans and compared it to the distribution of element insertions (presumably fixed) within the sequenced genome. Tc1 elements preferentially insert in regions with high recombination rates, whereas Tc3 and Tc5 do not. Although Tc1 and Tc3 both insert in TA dinucleotides, there is no clear relationship between the frequency of insertions and the TA dinucleotide density. There is a strong selection against TE insertions within coding regions: the probability that a TE will be fixed is at least 31 times lower in coding regions than in noncoding regions. Contrary to the prediction of theoretical models, we found that the selective pressure against TE insertions does not increase with the recombination rate. These findings indicate that the distribution of these three transposon families in the genome of C. elegans is determined essentially by just two factors: the pattern of insertions, which is a characteristic of each family, and the selection against insertions within coding regions.

Published
2003

45. A derived ZW chromosome system in Amborella trichopoda, the sister species to all other extant flowering plants

Author

Käfer, Jos, primary, Bewick, Adam, additional, Andres-Robin, Amélie, additional, Lapetoule, Garance, additional, Harkess, Alex, additional, Caïus, José, additional, Fogliani, Bruno, additional, Gâteblé, Gildas, additional, Ralph, Paula, additional, dePamphilis, Claude W., additional, Picard, Franck, additional, Scutt, Charlie P., additional, Leebens-Mack, James, additional, and Marais, Gabriel AB, additional

Published
2020
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