title: Species delimitation in the lichenized fungal genus Vulpicida (Parmeliaceae, Ascomycota) using gene concatenation and coalescent-based species tree approaches.
abstract: •
  
  
  OBJECTIVE
  Species boundaries in many organism groups are still in a state of flux, and for empirical species delimitation, finding appropriate character sets and analytical tools are among the greatest challenges. In the lichenized fungal genus Vulpicida, six morphologically circumscribed species have been distinguished, but phenotypic characters partly overlap for three of these and intermediate forms occur. We used a combination of phylogenetic strategies to delimit the species in this genus.•
  
  
  METHODS
  Five DNA loci were sequenced and analyzed. Single-locus gene trees and a five-locus concatenated phylogeny were constructed to assess current Vulpicida species. Species boundaries were inferred from molecular data using two coalescent-based species delimitation methods (BP&P and Brownie) and from species trees reconstructed with three different algorithms (*BEAST, BEST, and STEM).•
  
  
  RESULTS
  The two species restricted to North America, Vulpicida canadensis and V. viridis, are clearly distinct in all analyses. The four other traditionally accepted species form two strongly supported, closely related species-level lineages within the core group of the genus. On the basis of these results, we propose four instead of the current six species in the genus: V. canadensis, V. juniperinus, V. pinastri, and V. viridis, while V. tilesii and V. tubulosus are reduced to synonymy under V. juniperinus.•
  
  
  CONCLUSIONS
  Coalescent species delimitation and tree inference give consistent results for fully distinct Vulpicida species but not for diverging populations. Even the inconsistent results were informative, revealing developing isolation despite a complex history of recombination and incomplete lineage sorting.
authors.affiliation: Estonian Biocentre, Riia 23b 51010 Tartu, Estonia University of Tartu, Institute of Ecology and Earth Sciences, Department of Botany, Lai 38-40 51005 Tartu, Estonia.
authors.forename: Lauri
authors.initials: L
authors.lastname: Saag
authors.affiliation: University of Tartu, Institute of Ecology and Earth Sciences, Department of Botany, Lai 38-40 51005 Tartu, Estonia Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland.
authors.forename: Kristiina
authors.initials: K
authors.lastname: Mark
authors.affiliation: University of Tartu, Institute of Ecology and Earth Sciences, Department of Botany, Lai 38-40 51005 Tartu, Estonia.
authors.forename: Andres
authors.initials: A
authors.lastname: Saag
authors.affiliation: University of Tartu, Institute of Ecology and Earth Sciences, Department of Botany, Lai 38-40 51005 Tartu, Estonia.
authors.forename: Tiina
authors.initials: T
authors.lastname: Randlane
mesh_terms: D001203:Ascomycota / Q000235:genetics*; D004271:DNA, Fungal / Q000032:analysis*; D008011:Lichens / Q000235:genetics*; D009656:North America; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004271:DNA, Fungal
keywords: Ascomycota; Parmeliaceae; coalescent-based approach; gene concatenation; lichen; multilocus; species delimitation; species tree