Open Source Ferns

Joel H. Nitta

https://www.joelnitta.com

Joel H. Nitta, PhD

• 4th generation Japanese-American, now living in Japan
• Assoc. Prof. at Chiba University
• Research topic: the ecology and evolution of ferns

Photo: Jean-Yves Meyer

Why ferns?

Ferns are mysterious

Cryptogams

Fitton, Sarah Mary, and Elizabeth Fitton. “Plate 20: Cryptogamia.” In Conversations on Botany. London, England: Longman, Hurst, Rees, Orme, and Brown, 1817.
https://digital.sciencehistory.org/works/ks65hc299.
Public domain.

“We have the receipt of fern seed: we walk invisible”

Shakespeare, Henry IV Part I, Act 2, scene 1

Photo: Jose A. Campos
https://www.fernsoftheworld.com/2016/05/31/cheilanthes-hispanica/

Photo: Meredith Cosgrove
http://www.plantsystematics.org/imgs/meredith/r/Marsileaceae_Marsilea_drummondii_38654.html

Spores

Vascular tissue

Photo: Robbin Moran
http://www.plantsystematics.org/cgi-bin/dol/dol_show_link.pl?/imgs/robbin/r/Dryopteridaceae_Polystichum_concinnum_7548.html

Sigel, E.M. et al. (2018) Frontiers in Plant Science https://doi.org/10.3389/fpls.2018.01450.
CC BY 4.0, https://creativecommons.org/licenses/by/4.0/

Sigel, E.M. et al. (2018) Frontiers in Plant Science https://doi.org/10.3389/fpls.2018.01450.
CC BY 4.0, https://creativecommons.org/licenses/by/4.0/

Sporophyte

Gametophyte

Sigel, E.M. et al. (2018) Frontiers in Plant Science https://doi.org/10.3389/fpls.2018.01450.
CC BY 4.0, https://creativecommons.org/licenses/by/4.0/

DNA barcoding

Open source data

• DNA barcoding only works when there are reference data

• Open source software enables technical progress

• Open data enable scientific progress

https://ncbiinsights.ncbi.nlm.nih.gov/

The Fern Tree of Life (FTOL) project

• Goal: build a phylogenetic tree including all fern species on the planet (about ~12,000).

• Benefits from and gives back to open science

Nitta, Joel H., Eric Schuettpelz, Santiago Ramírez-Barahona, and Wataru Iwasaki. 2022. “An Open and Continuously Updated Fern Tree of Life.” Frontiers in Plant Sciences 13. https://doi.org/10.3389/fpls.2022.909768.

Building FTOL

• Download data from GenBank (global repository of DNA sequences), clean it, and analyze.

• Automate with code, repeat.

Growth of FTOL

• The initial publication of FTOL was the largest fern phylogeny to date (~6,000 species).

• Number of total fern sequences has steadily increased since the initial publication.

Nitta, Joel H., Eric Schuettpelz, Santiago Ramírez-Barahona, and Wataru Iwasaki. 2022. “An Open and Continuously Updated Fern Tree of Life.” Frontiers in Plant Sciences 13. https://doi.org/10.3389/fpls.2022.909768.

Research supported by FTOL

• Discovery of convergent evolution of extra-floral nectaries in ferns and flowering plants.

Suissa, J.S., Li, FW. & Moreau, C.S. Convergent evolution of fern nectaries facilitated independent recruitment of ant-bodyguards from flowering plants. Nat Commun 15, 4392 (2024). https://doi.org/10.1038/s41467-024-48646-x

Towards Open Taxonomy

• Taxonomy is the study of naming life
• Until very recently, taxonomies were published by a small number of experts

Pteridophyte Phylogeny Group (PPG)

• PPG seeks to democratize and accelerate the taxonomic process by using an open-source, community-driven model

Photo: Cheng-Wei Chen

Discussions hosted on GitHub

https://github.com/pteridogroup/ppg

Taxonomic decisions are made by vote

Sahashia stricta (Underw.) Li Bing Zhang & Liang Zhang Observed in Russian Federation by V.S. Volkotrub (licensed under http://creativecommons.org/licenses/by-nc/4.0/)

Taxonomy is continuously updated and openly available

… in collaboration with World Flora Online (WFO)

https://wfoplantlist.org/

Take-home messages

• Science thrives in the open.
• We need to incentivize maintenance of databases and software.
• Ferns are cool!

Acknowledgements

• Eric Schuettpelz
  

• Harald Schneider
  

• Carl Rothfels
  

• Michael Hassler
  

• …and the entire PPG community

• Japan Society for the Promotion of Science (16H06279, 22H04925, 22K1517)