Abstract Detail

Pteridology

Nitta, Joel [1], Schuettpelz, Eric [2], Ramírez-Barahona, Santiago [3], Iwasaki, Wataru [1].

An Open and Continuously Updated Fern Tree of Life (FTOL).

Ferns, with about 12,000 species, are the second most diverse clade 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have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated.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 5,563 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 65 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. 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. We intend for FTOL to be an open resource, meaning 1) it is available for anybody to use for their own research, and 2) anybody may contribute changes to improve FTOL for the benefit of all. Accordingly, this presentation will particularly focus on how researchers can use and contribute to FTOL.

Related Links:
FTOL website
Github
Preprint

1 - The University of Tokyo, Department of Integrated Biosciences, Graduate School of Frontier Sciences, Kashiwa, Chiba, 277-0882, Japan
2 - National Museum of Natural History, Smithsonian Institution, Department of Botany, USA
3 - Universidad Nacional Autónoma de México, Departamento de Botánica, Mexico City, Mexico

Keywords:
phylogeny
plastome
PPG I
pteridophyte
rbcL.

Presentation Type: Oral Paper
Number: PTR2001
Abstract ID:364
Candidate for Awards:Edgar T. Wherry award