title: Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta.
abstract: Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and computational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. We present here a population genomic study of a phylogenetic species in the Neurospora discreta species complex, based on the resequencing of full genomes (~37 Mb) for 52 fungal isolates from nine sites in three continents. Population structure analyses revealed two distinct lineages in South-East Asia, and three lineages in North America/Europe with a broad longitudinal and latitudinal range and limited admixture between lineages. Genome scans for selective sweeps and comparisons of the genomic landscapes of diversity and recombination provided no support for a role of selection at linked sites on genomic heterogeneity in levels of divergence between lineages. However, demographic inference indicated that the observed genomic heterogeneity in divergence was generated by varying rates of gene flow between lineages following a period of isolation. Many putative cases of exchange of genetic material between phylogenetically divergent fungal lineages have been discovered, and our work highlights the quantitative importance of genetic exchanges between more closely related taxa to the evolution of fungal genomes. Our study also supports the role of allopatric isolation as a driver of diversification in saprobic microbes.
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.|Ecologie Systematique Evolution, Université Paris Sud, Batiment 360, 91405, Orsay, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Gladieux
authors.affiliation: Department of Biology, Stanford University, Stanford, CA, USA.
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Wilson
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.|Ecole Polytechnique, Route de Saclay, 91128, Palaiseau, France.
authors.forename: Fanny
authors.initials: F
authors.lastname: Perraudeau
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
authors.forename: Liliam A
authors.initials: LA
authors.lastname: Montoya
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
authors.forename: David
authors.initials: D
authors.lastname: Kowbel
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Hann-Soden
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
authors.forename: Monika
authors.initials: M
authors.lastname: Fischer
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
authors.forename: Iman
authors.initials: I
authors.lastname: Sylvain
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
authors.forename: David J
authors.initials: DJ
authors.lastname: Jacobson
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
authors.forename: John W
authors.initials: JW
authors.lastname: Taylor
mesh_terms: D001210:Asia, Southeastern; D004271:DNA, Fungal / Q000235:genetics; D005060:Europe; D005390:Fires; D051456:Gene Flow; D049810:Genetic Speciation; D005828:Genetics, Population; D016681:Genome, Fungal; D008957:Models, Genetic; D009491:Neurospora / Q000235:genetics*; D009656:North America; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D060047:Reproductive Isolation; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal
keywords: Ascomycete; hybridization; resequencing; secondary contact; selective sweeps; speciation