title: Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes.
abstract: Fungi are ideal model organisms for dissecting the genomic bases of adaptive divergence in eukaryotes. They have simple morphologies and small genomes, occupy contrasting, well-identified ecological niches and tend to have short generation times, and many are amenable to experimental approaches. Fungi also display diverse lifestyles, from saprotrophs to pathogens or mutualists, and they play extremely important roles in both ecosystems and human activities, as wood decayers, mycorrhizal fungi, lichens, endophytes, plant and animal pathogens, and in fermentation or drug production. We review here recent insights into the patterns and mechanisms of adaptive divergence in fungi, including sources of divergence, genomic variation and, ultimately, speciation. We outline the various ecological sources of divergent selection and genomic changes, showing that gene loss and changes in gene expression and in genomic architecture are important adaptation processes, in addition to the more widely recognized processes of amino acid substitution and gene duplication. We also review recent findings regarding the interspecific acquisition of genomic variation and suggesting an important role for introgression, hybridization and horizontal gene transfers (HGTs). We show that transposable elements can mediate several of these genomic changes, thus constituting important factors for adaptation. Finally, we review the consequences of divergent selection in terms of speciation, arguing that genetic incompatibilities may not be as widespread as generally thought and that pleiotropy between adaptation and reproductive isolation is an important route of speciation in fungal pathogens.
authors.affiliation: Ecologie, Systématique et Evolution, UMR8079, University of Paris-Sud, Orsay, 91405, France; Ecologie, Systématique et Evolution, CNRS, UMR8079, Orsay, 91405, France; Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA.
authors.forename: Pierre
authors.initials: P
authors.lastname: Gladieux
authors.forename: Jeanne
authors.initials: J
authors.lastname: Ropars
authors.forename: Hélène
authors.initials: H
authors.lastname: Badouin
authors.forename: Antoine
authors.initials: A
authors.lastname: Branca
authors.forename: Gabriela
authors.initials: G
authors.lastname: Aguileta
authors.forename: Damien M
authors.initials: DM
authors.lastname: de Vienne
authors.forename: Ricardo C
authors.initials: RC
authors.lastname: Rodríguez de la Vega
authors.forename: Sara
authors.initials: S
authors.lastname: Branco
authors.forename: Tatiana
authors.initials: T
authors.lastname: Giraud
mesh_terms: D000220:Adaptation, Biological; D005075:Biological Evolution; D004251:DNA Transposable Elements; D056890:Eukaryota / Q000235:genetics; D005658:Fungi / Q000235:genetics*; D022761:Gene Transfer, Horizontal; D049810:Genetic Speciation; D023281:Genomics; D006824:Hybridization, Genetic; D060047:Reproductive Isolation
chemical_list: D004251:DNA Transposable Elements
keywords: Coccidioides; Neurospora; Penicillium; Saccharomyces; competition; effector; gene regulation; genetic incompatibilities; genomic islands; local adaptation; positive selection; yeast