title: Neogene-dominated diversification in neotropical montane lichens: dating divergence events in the lichen-forming fungal genus Oropogon (Parmeliaceae).
abstract: OBJECTIVE
  Diversification in neotropical regions has been attributed to both Tertiary geological events and Pleistocene climatic fluctuations. However, the timing and processes driving speciation in these regions remain unexplored in many important groups. Here, we address the timing of diversification in the neotropical lichenized fungal genus Oropogon (Ascomycota) and assess traditional species boundaries.
  
  
  METHODS
  We analyzed sequence data from three loci to assess phenotypically circumscribed Oropogon species from the Oaxacan Highlands, Mexico. We provide a comparison of dated divergence estimates between concatenated gene trees and a calibrated multilocus species-tree using substitution rates for two DNA regions. We also compare estimates from a data set excluding ambiguously aligned regions and a data set including the hyper-variable regions in two ribosomal markers.
  
  
  RESULTS
  Phylogenetic reconstructions were characterized by well-supported monophyletic clades corresponding to traditionally circumscribed species, with the exception of a single taxon. Divergence estimates indicate that most diversification of the sampled Oropogon species occurred throughout the Oligocene and Miocene, although diversification of a single closely related clade appears to have occurred during the late Pliocene and into the Pleistocene. Divergence estimates calculated from a data set with ambiguously aligned regions removed were much more recent than those from the full data set.
  
  
  CONCLUSIONS
  Overall, our analyses place the majority of divergence events of Oropogon species from the Oaxacan Highlands within the Neogene and provide strong evidence that climatic changes during the Pleistocene were not a major factor driving speciation in the lichenized genus Oropogon in neotropical highlands.
authors.affiliation: The Field Museum, Department of Botany, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, USA. sleavitt@fi eldmuseum.org
authors.forename: Steven D
authors.initials: SD
authors.lastname: Leavitt
authors.forename: Theodore L
authors.initials: TL
authors.lastname: Esslinger
authors.forename: H Thorsten
authors.initials: HT
authors.lastname: Lumbsch
mesh_terms: D001203:Ascomycota / Q000145:classification / Q000235:genetics*; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D005800:Genes, Fungal / Q000235:genetics*; D014644:Genetic Variation; D008011:Lichens / Q000382:microbiology*; D008800:Mexico; D008969:Molecular Sequence Data; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013997:Time Factors; D014329:Tropical Climate
chemical_list: D004271:DNA, Fungal