title: Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species.
abstract: •
  
  
  OBJECTIVE
  Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts, inhabiting healthy leaves and stems of all major lineages of plants. Together, they comprise immense species richness, but little is known about the fundamental processes that generate their diversity. Exploration of their population structure is needed, especially with regard to geographic distributions and host affiliations.•
  
  
  METHODS
  We take a multilocus approach to examine genetic variation within and among populations of Lophodermium australe, an endophytic fungus commonly associated with healthy foliage of pines in the southeastern United States. Sampling focused on two pine species ranging from montane to coastal regions of North Carolina and Virginia.•
  
  
  RESULTS
  Our sampling revealed two genetically distinct groups within Lophodermium australe. Our analysis detected less than one migrant per generation between them, indicating that they are distinct species. The species comprising the majority of isolates (major species) demonstrated a panmictic structure, whereas the species comprising the minority of isolates (cryptic species) demonstrated isolation by distance. Distantly related pine species hosted the same Lophodermium species, and host species did not influence genetic structure.•
  
  
  CONCLUSIONS
  We present the first evidence for isolation by distance in a foliar fungal endophyte that is horizontally transmitted. Cryptic species may be common among microbial symbionts and are important to delimit when exploring their genetic structure and microevolutionary processes. The hyperdiversity of endophytic fungi may be explained in part by cryptic species without apparent ecological and morphological differences as well as genetic diversification within rare fungal species across large spatial scales.
authors.affiliation: University of California-Santa Barbara, Santa Barbara, California 93106 USA Duke University, Durham, North Carolina 27708 USA North Carolina State University, Raleigh, North Carolina 27695 USA.
authors.forename: Ryoko
authors.initials: R
authors.lastname: Oono
authors.affiliation: Duke University, Durham, North Carolina 27708 USA.
authors.forename: François
authors.initials: F
authors.lastname: Lutzoni
authors.affiliation: University of Arizona, Tucson, Arizona 85721 USA.
authors.forename: A Elizabeth
authors.initials: AE
authors.lastname: Arnold
authors.affiliation: Duke University, Durham, North Carolina 27708 USA.
authors.forename: Laurel
authors.initials: L
authors.lastname: Kaye
authors.affiliation: University of Arizona, Tucson, Arizona 85721 USA.
authors.forename: Jana M
authors.initials: JM
authors.lastname: U'Ren
authors.affiliation: University of Minnesota, St. Paul, Minnesota 55108 USA.
authors.forename: Georgiana
authors.initials: G
authors.lastname: May
authors.affiliation: North Carolina State University, Raleigh, North Carolina 27695 USA.
authors.forename: Ignazio
authors.initials: I
authors.lastname: Carbone
mesh_terms: D001203:Ascomycota / Q000235:genetics*; D044822:Biodiversity; D005075:Biological Evolution; D060026:Endophytes / Q000235:genetics*; D014644:Genetic Variation; D005828:Genetics, Population; D009657:North Carolina; D010802:Phylogeny; D028223:Pinus / Q000382:microbiology*; D018515:Plant Leaves / Q000382:microbiology; D013559:Symbiosis; D014768:Virginia
keywords: Lophodermium; Pinus; Rhytismataceae; diversity; foliar fungal endophyte; speciation