{"id":21074,"date":"2025-07-11T16:31:29","date_gmt":"2025-07-11T14:31:29","guid":{"rendered":"https:\/\/www.egce.universite-paris-saclay.fr\/?p=21074"},"modified":"2025-07-11T16:33:09","modified_gmt":"2025-07-11T14:33:09","slug":"offre-de-stage-m2-2","status":"publish","type":"post","link":"https:\/\/www.egce.universite-paris-saclay.fr\/?p=21074","title":{"rendered":"Offre de stage M2"},"content":{"rendered":"\n

Mod\u00e9lisation de l\u2019amplification des \u00e9l\u00e9ments transposables lors des expansions g\u00e9ographiques<\/strong><\/p>\n\n\n\n

Contexte scientifique<\/strong><\/p>\n\n\n\n

Les \u00e9l\u00e9ments transposables sont des s\u00e9quences d\u2019ADN pr\u00e9sentes dans le g\u00e9nome de presque tous les organismes vivants, et capables de s\u2019y d\u00e9placer et de s\u2019y multiplier. Souvent consid\u00e9r\u00e9s comme des parasites du g\u00e9nome, les \u00e9l\u00e9ments transposables sont mutag\u00e8nes et leur activit\u00e9 est probablement co\u00fbteuse; ils pourraient cependant \u00eatre \u00e0 l\u2019origine de variants g\u00e9n\u00e9tiques potentiellement utiles \u00e0 l\u2019adaptation. Les \u00e9l\u00e9ments transposables sont tr\u00e8s divers et leur nombre diff\u00e8re beaucoup selon les g\u00e9nomes. Les raisons qui expliquent l\u2019in\u00e9gale r\u00e9partition de ces \u00e9l\u00e9ments entre les esp\u00e8ces sont mal comprises; elles impliquent probablement des diff\u00e9rences dans les m\u00e9canismes de la r\u00e9gulation de la transposition, mais aussi l\u2019histoire r\u00e9cente, et en particulier la d\u00e9mographie, des diff\u00e9rentes esp\u00e8ces. <\/p>\n\n\n\n

L\u2019aire de r\u00e9partition des esp\u00e8ces change au cours du temps. Les esp\u00e8ces exotiques envahissantes, comme le moustique tigre ou le frelon asisatique, inconnues dans nos contr\u00e9es jusqu\u2019\u00e0 r\u00e9cemment, en sont des exemples frappants. Mais on sait aujourd’hui que l\u2019essentiel de la faune et de la flore qui nous entoure a \u00e9galement r\u00e9cemment connu des modifications consid\u00e9rables de sa distribution : lors du dernier maximum glaciaire, la plupart des esp\u00e8ces europ\u00e9ennes temp\u00e9r\u00e9es \u00e9taient confin\u00e9es dans les p\u00e9ninsules du Sud du continent. A partir de ces refuges glaciaires, elles ont colonis\u00e9 le Nord de l\u2019Europe \u00e0 mesure que le climat se r\u00e9chauffait (\u00e0 partir de -15 000 ans) et ainsi connu d\u2019importantes expansions g\u00e9ographiques.<\/p>\n\n\n\n

Les expansions g\u00e9ographiques sont caract\u00e9ris\u00e9es par une d\u00e9mographie particuli\u00e8re : des goulots d\u2019\u00e9tranglement (r\u00e9ductions importantes d\u2019effectifs) successifs se d\u00e9roulent sur le front d\u2019expansion. Ces goulots d\u2019\u00e9tranglement engendrent une forte d\u00e9rive g\u00e9n\u00e9tique, susceptible de favoriser la prolif\u00e9ration de mutations d\u00e9l\u00e9t\u00e8res et donc des \u00e9l\u00e9ments transposables au sein des populations du front. La colonisation de nouveaux habitats va \u00e9galement n\u00e9cessiter une adaptation g\u00e9n\u00e9tique, et donc possiblement la fixation rapide de nouveaux variants. Ces conditions semblent \u00e9galement favorables \u00e0 l\u2019accumulation d\u2019\u00e9l\u00e9ments transposables; toutefois, il n\u2019existe pas de mod\u00e8les formels en g\u00e9n\u00e9tique et g\u00e9nomique des populations qui permettraient de fonder cette hypoth\u00e8se sur des bases th\u00e9oriques solides. <\/p>\n\n\n\n

Objectifs<\/strong><\/p>\n\n\n\n

L\u2019objectif de ce stage serait donc d\u2019\u00e9tudier, par des simulations num\u00e9riques, le processus d\u2019accumulation des \u00e9l\u00e9ments transposables dans la vague de colonisation d\u2019une esp\u00e8ce en phase d\u2019expansion g\u00e9ographique. Le projet se base sur un logiciel de simulation individu-centr\u00e9 d\u00e9j\u00e0 disponible, qui sera exploit\u00e9 dans un contexte spatial explicite o\u00f9 des habitats disponibles sont progressivement colonis\u00e9s par des migrants issus des populations d\u00e9j\u00e0 \u00e9tablies. Le stage devra r\u00e9pondre aux questions suivantes: les simulations confirment-elles une augmentation du nombre de copies d\u2019\u00e9l\u00e9ments transposables \u00e0 la marge de l\u2019aire de r\u00e9partition? Quels sont les effets des param\u00e8tres du mod\u00e8les (taux de transposition, taux de migration, taille des populations) sur cette accumulation? Sur combien de temps et sur quelle distance g\u00e9ographique cette accumulation peut-elle \u00eatre d\u00e9tect\u00e9e? <\/p>\n\n\n\n

Profil<\/strong><\/p>\n\n\n\n

Nous recherchons un.e \u00e9tudiant.e avec une formation solide en g\u00e9n\u00e9tique et g\u00e9nomique des populations, avec une attirance pour les questions th\u00e9oriques. Le logiciel de simulation (C++) \u00e9tant d\u00e9j\u00e0 disponible, le stage n\u2019impliquera pas de d\u00e9veloppement logiciel \u00e0 proprement parler, mais l\u2019adaptation ou l\u2019optimisation du code pourra \u00eatre envisag\u00e9e. Une ma\u00eetrise des outils informatiques (R \/ python \/ Unix) sera appr\u00e9ci\u00e9e. Le stage se d\u00e9roulerait sur une p\u00e9riode de 6 mois, id\u00e9alement de janvier \u00e0 juin 2026. <\/p>\n\n\n\n

Laboratoires d\u2019accueil<\/strong><\/p>\n\n\n\n

Le stage sera co-encadr\u00e9 par Arnaud Le Rouzic (CR CNRS, EGCE, IDEEV, Universit\u00e9 Paris-Saclay) et Matthieu Boulesteix (MdC Universit\u00e9 Lyon I). L\u2019\u00e9tudiant(e) pourra \u00eatre bas\u00e9.e \u00e0 Gif-sur-Yvette ou \u00e0 Lyon. <\/p>\n\n\n\n

Contacts: <\/p>\n\n\n\n

Arnaud Le Rouzic<\/a>, arnaud.le-rouzic@universite-paris-saclay.fr<\/p>\n\n\n\n

Matthieu Boulesteix<\/a>, matthieu.boulesteix@univ-lyon1.fr<\/p>\n\n\n\n

R\u00e9f\u00e9rences bibliographiques:<\/strong><\/p>\n\n\n\n

Litt\u00e9rature sur le sujet:<\/em><\/p>\n\n\n\n

Dolgin, E. S., & Charlesworth, B. (2008). The effects of recombination rate on the distribution and abundance of transposable elements. Genetics<\/em>, 178<\/em>(4), 2169-2177.<\/p>\n\n\n\n

Excoffier, L., & Ray, N. (2008). Surfing during population expansions promotes genetic revolutions and structuration. Trends in ecology & evolution<\/em>, 23<\/em>(7), 347-351.<\/p>\n\n\n\n

Hallatschek, O., & Nelson, D. R. (2008). Gene surfing in expanding populations. Theoretical population biology<\/em>, 73<\/em>(1), 158-170.<\/p>\n\n\n\n

Peischl, S., Dupanloup, I., Kirkpatrick, M., & Excoffier, L. (2013). On the accumulation of deleterious mutations during range expansions. Molecular Ecology, 22(24), 5972-5982. https:\/\/doi.org\/10.1111\/mec.12524<\/p>\n\n\n\n

Publication sur des sujets proches des \u00e9quipes d\u2019accueil:<\/em><\/p>\n\n\n\n

Le Rouzic, A., & Capy, P. (2005). The first steps of transposable elements invasion: parasitic strategy vs. genetic drift. Genetics<\/em>, 169<\/em>(2), 1033-1043.<\/p>\n\n\n\n

M\u00e9rel, V., Gibert, P., Buch, I., Rodriguez Rada, V., Estoup, A., Gautier, M., Fablet, M., Boulesteix, M., & Vieira, C. (2021). The worldwide invasion of Drosophila suzukii is accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions. Molecular biology and evolution, 38(10), 4252-4267.<\/p>\n\n\n\n

Tomar, S. S., Hua-Van, A., & Le Rouzic, A. (2023). A population genetics theory for piRNA-regulated transposable elements. Theoretical Population Biology<\/em>, 150<\/em>, 1-13.<\/p>\n\n\n\n

Le Rouzic, A., & Hua-Van, A. (2024). Genome Invasion Dynamics. Transposable Elements and Genome Evolution<\/em>, 175-191.<\/p>\n","protected":false},"excerpt":{"rendered":"

Mod\u00e9lisation de l\u2019amplification des \u00e9l\u00e9ments transposables lors des expansions g\u00e9ographiques Contexte scientifique Les \u00e9l\u00e9ments transposables sont des s\u00e9quences d\u2019ADN pr\u00e9sentes dans le g\u00e9nome de presque tous les organismes vivants, et capables de s\u2019y d\u00e9placer et de s\u2019y multiplier. Souvent consid\u00e9r\u00e9s comme des parasites du g\u00e9nome, les \u00e9l\u00e9ments transposables sont mutag\u00e8nes et leur activit\u00e9 est probablement […]<\/p>\n","protected":false},"author":45,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"_themeisle_gutenberg_block_has_review":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[30,504,28],"tags":[],"class_list":["post-21074","post","type-post","status-publish","format-standard","hentry","category-master-ii","category-pole-genomes","category-stages"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/www.egce.universite-paris-saclay.fr\/index.php?rest_route=\/wp\/v2\/posts\/21074","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.egce.universite-paris-saclay.fr\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.egce.universite-paris-saclay.fr\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.egce.universite-paris-saclay.fr\/index.php?rest_route=\/wp\/v2\/users\/45"}],"replies":[{"embeddable":true,"href":"https:\/\/www.egce.universite-paris-saclay.fr\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=21074"}],"version-history":[{"count":1,"href":"https:\/\/www.egce.universite-paris-saclay.fr\/index.php?rest_route=\/wp\/v2\/posts\/21074\/revisions"}],"predecessor-version":[{"id":21075,"href":"https:\/\/www.egce.universite-paris-saclay.fr\/index.php?rest_route=\/wp\/v2\/posts\/21074\/revisions\/21075"}],"wp:attachment":[{"href":"https:\/\/www.egce.universite-paris-saclay.fr\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=21074"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.egce.universite-paris-saclay.fr\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=21074"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.egce.universite-paris-saclay.fr\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=21074"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}