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An Open and Continuously Updated Fern Tree of Life

View ORCID ProfileJoel H. Nitta, View ORCID ProfileEric Schuettpelz, View ORCID ProfileSantiago Ramírez-Barahona, View ORCID ProfileWataru Iwasaki
doi: https://doi.org/10.1101/2022.03.31.486640
Joel H. Nitta
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
9Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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  • For correspondence: joelnitta@gmail.com
Eric Schuettpelz
2Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States
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Santiago Ramírez-Barahona
3Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Wataru Iwasaki
1Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
4Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
5Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
6Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
7Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
8Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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1 Abstract

Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated.

Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification.

The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies.

FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Correct missing bold text in Figure 3 Correct various typos

  • https://github.com/fernphy/ftol

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted July 21, 2022.
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An Open and Continuously Updated Fern Tree of Life
Joel H. Nitta, Eric Schuettpelz, Santiago Ramírez-Barahona, Wataru Iwasaki
bioRxiv 2022.03.31.486640; doi: https://doi.org/10.1101/2022.03.31.486640
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An Open and Continuously Updated Fern Tree of Life
Joel H. Nitta, Eric Schuettpelz, Santiago Ramírez-Barahona, Wataru Iwasaki
bioRxiv 2022.03.31.486640; doi: https://doi.org/10.1101/2022.03.31.486640

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