Carl J Rothfels1, Fay-Wei Li2, Erin M Sigel3, Layne Huiet2, Anders Larsson4, Dylan O Burge5, Markus Ruhsam6, Michael Deyholos7, Douglas E Soltis8, C Neal Stewart9, Shane W Shaw10, Lisa Pokorny11, Tao Chen12, Claude dePamphilis13, Lisa DeGironimo14, Li Chen15, Xiaofeng Wei15, Xiao Sun15, Petra Korall4, Dennis W Stevenson14, Sean W Graham16, Gane K-S Wong17, Kathleen M Pryer2. 1. Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada. 2. Department of Biology, Duke University, Durham, North Carolina 27708 USA. 3. Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, P.O. Box 37012 Washington, District of Columbia 20013-7012 USA. 4. Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden. 5. California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118 USA. 6. Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK. 7. Department of Biology, University of British Columbia, Okanagan Campus, 1177 Research Road, Kelowna, British Columbia V1V 1V7, Canada. 8. Florida Museum of Natural History, Department of Biology, and the Genetics Institute. University of Florida. Gainesville, Florida 32611 USA. 9. Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA. 10. Orleans, Vermont 05860 USA. 11. Departamento de Biodiversidad y Conservación, Real Jardín Botánico-Consejo Superior de Investigaciones Científicas, 28014 Madrid, Spain. 12. Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China. 13. Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 USA. 14. The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA. 15. BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China. 16. Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada. 17. Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.
Abstract
UNLABELLED: • PREMISE OF THE STUDY: 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.• KEY 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.
UNLABELLED: • PREMISE OF THE STUDY: 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.• KEY 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: Kangshan Mao; Markus Ruhsam; Yazhen Ma; Sean W Graham; Jianquan Liu; Philip Thomas; Richard I Milne; Peter M Hollingsworth Journal: Ann Bot Date: 2019-01-01 Impact factor: 4.357
Authors: Michael R May; Dori L Contreras; Michael A Sundue; Nathalie S Nagalingum; Cindy V Looy; Carl J Rothfels Journal: Syst Biol Date: 2021-10-13 Impact factor: 15.683
Authors: Fay-Wei Li; Carl J Rothfels; Michael Melkonian; Juan C Villarreal; Dennis W Stevenson; Sean W Graham; Gane K-S Wong; Sarah Mathews; Kathleen M Pryer Journal: Front Plant Sci Date: 2015-08-12 Impact factor: 5.753