title: The evolutionary history of ferns inferred from 25 low-copy nuclear genes.
abstract: •
  
  
  OBJECTIVE
  Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.•
  
  
  METHODS
  Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.•
  
  
  RESULTS
  Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.•
  
  
  CONCLUSIONS
  Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
authors.affiliation: Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada.
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Rothfels
authors.affiliation: Department of Biology, Duke University, Durham, North Carolina 27708 USA.
authors.forename: Fay-Wei
authors.initials: FW
authors.lastname: Li
authors.affiliation: Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, P.O. Box 37012 Washington, District of Columbia 20013-7012 USA.
authors.forename: Erin M
authors.initials: EM
authors.lastname: Sigel
authors.affiliation: Department of Biology, Duke University, Durham, North Carolina 27708 USA.
authors.forename: Layne
authors.initials: L
authors.lastname: Huiet
authors.affiliation: Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Anders
authors.initials: A
authors.lastname: Larsson
authors.affiliation: California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118 USA.
authors.forename: Dylan O
authors.initials: DO
authors.lastname: Burge
authors.affiliation: Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK.
authors.forename: Markus
authors.initials: M
authors.lastname: Ruhsam
authors.affiliation: Department of Biology, University of British Columbia, Okanagan Campus, 1177 Research Road, Kelowna, British Columbia V1V 1V7, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Deyholos
authors.affiliation: Florida Museum of Natural History, Department of Biology, and the Genetics Institute. University of Florida. Gainesville, Florida 32611 USA.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Soltis
authors.affiliation: Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA.
authors.forename: C Neal
authors.initials: CN
authors.lastname: Stewart
authors.affiliation: Orleans, Vermont 05860 USA.
authors.forename: Shane W
authors.initials: SW
authors.lastname: Shaw
authors.affiliation: Departamento de Biodiversidad y Conservación, Real Jardín Botánico-Consejo Superior de Investigaciones Científicas, 28014 Madrid, Spain.
authors.forename: Lisa
authors.initials: L
authors.lastname: Pokorny
authors.affiliation: Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Chen
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 USA.
authors.forename: Claude
authors.initials: C
authors.lastname: dePamphilis
authors.affiliation: The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: DeGironimo
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Wei
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Sun
authors.affiliation: Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden.
authors.forename: Petra
authors.initials: P
authors.lastname: Korall
authors.affiliation: The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA.
authors.forename: Dennis W
authors.initials: DW
authors.lastname: Stevenson
authors.affiliation: Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada.
authors.forename: Sean W
authors.initials: SW
authors.lastname: Graham
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.
authors.forename: Gane K-S
authors.initials: GK
authors.lastname: Wong
authors.affiliation: Department of Biology, Duke University, Durham, North Carolina 27708 USA.
authors.forename: Kathleen M
authors.initials: KM
authors.lastname: Pryer
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D029624:Ferns / Q000145:classification / Q000235:genetics*; D018628:Gene Dosage; D056426:Genetic Loci; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D018744:DNA, Plant
keywords: Equisetum; codon models; curated phylogenomics; divergence time dating; fern chronogram; incomplete lineage sorting; low-copy nuclear gene; model selection; monilophytes; transcriptome