title: Resolving evolutionary relationships in lichen-forming fungi using diverse phylogenomic datasets and analytical approaches.
abstract: Evolutionary histories are now being inferred from unprecedented, genome-scale datasets for a broad range of organismal groups. While phylogenomic data has helped in resolving a number of difficult, long-standing questions, constructing appropriate datasets from genomes is not straightforward, particularly in non-model groups. Here we explore the utility of phylogenomic data to infer robust phylogenies for a lineage of closely related lichen-forming fungal species. We assembled multiple, distinct nuclear phylogenomic datasets, ranging from ca. 25 Kb to 16.8 Mb and inferred topologies using both concatenated gene tree approaches and species tree methods based on the multispecies coalescent model. In spite of evidence for rampant incongruence among individual loci, these genome-scale datasets provide a consistent, well-supported phylogenetic hypothesis using both concatenation and multispecies coalescent approaches (ASTRAL-II and SVDquartets). However, the popular full hierarchical coalescent approach implemented in *BEAST provided inconsistent inferences, both in terms of nodal support and topology, with smaller subsets of the phylogenomic data. While comparable, well-supported topologies can be accurately inferred with only a small fraction of the overall genome, consistent results across a variety of datasets and methodological approaches provide reassurance that phylogenomic data can effectively be used to provide robust phylogenies for closely related lichen-forming fungal lineages.
authors.affiliation: Integrative Research Center, The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605, USA.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Leavitt
authors.affiliation: Integrative Research Center, The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605, USA.
authors.forename: Felix
authors.initials: F
authors.lastname: Grewe
authors.affiliation: Integrative Research Center, The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605, USA.|University of Illinois at Chicago, Department of Biological Sciences, 900 West Taylor St. #1016, M/C 066, Chicago, IL 60612, USA.
authors.forename: Todd
authors.initials: T
authors.lastname: Widhelm
authors.affiliation: University of Trieste, Department of Life Sciences, via Giorgieri 10, 34127-Trieste, Italy.
authors.forename: Lucia
authors.initials: L
authors.lastname: Muggia
authors.affiliation: Integrative Research Center, The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Wray
authors.affiliation: Integrative Research Center, The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605, USA.
authors.forename: H Thorsten
authors.initials: HT
authors.lastname: Lumbsch
mesh_terms: D001203:Ascomycota / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D001499:Bayes Theorem; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D005658:Fungi / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D016681:Genome, Fungal / Q000235:genetics; D023281:Genomics / Q000379:methods*; D005843:Geography; D008011:Lichens / Q000382:microbiology*; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014481:United States
chemical_list: D004271:DNA, Fungal; D004275:DNA, Ribosomal