Sonia Guillou's research while affiliated with Université de Montpellier and other places

... Growing evidence suggests that this decision matters, but it can be difficult to know a priori whether to assume a particular gene tree or the overall species tree, a specific set of gene trees, or even every possible gene tree. For example, many studies either assume a single specieslevel phylogeny that has been estimated using coalescent-based (Doña and Johnson, 2023) or traditional concatenation approaches (Hensen et al. 2023), or a single gene tree (e.g., Ross et al. 2004;Al-Kahtani et al. 2004;Kamilar and Cooper 2013;Adams et al. 2014;Gu 2016;Dunn et al. 2018;Chen et al. 2023) to model trait evolution. However, this assumption may (Dimayacyac et al. 2023) or may not (Hahn and Nakhleh 2016a) be the best strategy. ...

... Indeed, several fungal species carry extensive non-recombining DNA fragments around MAT loci. Recombination suppression can range from hundreds of kbp (kilo base pairs) to several Mbp (mega base pairs) and lead to genetic degeneration [5,9], such as in Neurospora tetrasperma [10], Podospora anserina [11], Schizothecium tetrasporum [12], Agaricus bisporus [13], Ustilago hordei [14], several species of Microbotryum [8,15] and Cryptococcus spp. [16,17]. ...

... GBS has been widely used to analyze the genetic diversity of rice [37], olive [38] and Chinese chestnut (Castanea mollissima Blume) [39], which is a convenient and costeffective approach [40,41]. We used stringent filtering criteria to generate 390.30 ...

... Indeed, in many fungi, two gametes can form a new individual only if they carry different mating types, but there is no sexual antagonism or other form of antagonistic selection between cells of opposite mating types; the cells of different mating types do not show contrasted phenotypes or footprints of diversifying selection (Bazzicalupo et al., 2019). Yet, evolutionary strata have been documented on the mating-type chromosomes of multiple fungi, with recombination suppression extending stepwise beyond mating-type determining genes (Fraser et al., 2004, Menkis et al., 2008, Branco et al., 2017, Branco et al., 2018, Hartmann, Duhamel, et al., 2021, Hartmann, Ament-Velásquez, et al., 2021, Vittorelli et al., 2023. Evolutionary strata have also been reported around other supergenes, i.e., large genomic regions encompassing multiple genes linked by recombination suppression, such as in ants and butterflies (Yan et al., 2020, Jay et al., 2021. ...