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

Phylogenies are essential to biology

Automated pipelines enable building large trees

Problem 1: tradeoff between scalability and accuracy

• Any automated pipeline must make shortcuts and assumptions

• Manual inspection of all sequences would lead to high-quality results, but does not scale

Problem 2: tree built today will be out-of-date tomorrow

• Due to the rapid accumulation of data on GenBank

Our approach: combine automation with customization

Goal: construct a pipeline to generate a maximally sampled, high taxonomic quality phylogeny of ferns

Why ferns?

A large, diverse, ecologically important group of plants

Much more tractable than seed plants (angiosperms):

• Ferns: ca. 12,000 species, 40-50% sequenced

• Seed plants: ca. 350,000 species, 20% sequenced

Sanger-sequenced plastid genes = workhorse of fern molecular systematics

GenBank mining

Sanger: 7 commonly used loci

• Genes: atpA, atpB, matK, rbcL, rps4
• Spacers: trnL–trnF, rps4–trnS
• ca. 5,100 species

Plastomes

• 77 single-copy genes + 2 spacers
• ca. 500 species

GenBank mining

• Download data to local database using restez* R package

• Use superCRUNCH (Portik and Wiens 2020) to extract sequences without relying on annotations

Taxonomic name resolution

• Use World Ferns (Hassler 2022) as basis for new, fern-specific taxonomic database, pteridocat

• Resolve GenBank species names to pteridocat using taxastand* R package

Automated cleaning

• Run all-by-all BLAST (Camacho et al. 2009)

• Any query matching the wrong family is excluded as mis-ID

Phylogenetic analysis: backbone

• Align plastome sequences with MAFFT (Katoh et al. 2002) (544 species x 74,883 bp, 12.1% missing)

• Infer tree using ML in IQ-TREE (Nguyen et al. 2015) (concatenated matrix, no paritioning)

Phylogenetic analysis: full tree

• Align Sanger sequences with MAFFT (5,582 species x 12,716 bp, 77% missing)

• Infer tree in IQ-TREE (concatenated matrix, no paritioning) with plastome tree as constraint

Revisiting the timeline of fern diversification

• 51 fossils (2x more than previous)

• Pushes back stem ages for most families ca. 10-30 my

• Suggests ferns did not diversify “in the shadow” of angiosperms

Older stem
ages for most
families

Web portal

https://fernphy.github.io/

• Data downloads

• Shiny app for exploring data

R package ftolr

https://github.com/fernphy/ftolr

• Read tree and data (alignments) directly into R

• Options for outgroups, rooting, locus selection, etc.

library(ftolr)
ft_tree(drop_og = TRUE)

Phylogenetic tree with 5582 tips and 5581 internal nodes.

Tip labels:
  Acrostichum_danaeifolium, Acrostichum_speciosum, Acrostichum_aureum, Ceratopteris_richardii, Ceratopteris_cornuta, Ceratopteris_shingii, ...
Node labels:
  100/100, 100/100, 100, 100/100, 100, 100/100, ...

Rooted; includes branch lengths.

Community involvement

Consulted with a taxonomic expert on family Thelypteridaceae (S. Fawcett) between v1.0.0 and v1.1.0

• Number of non-monophyletic genera dropped from 16 to 7

FTOL hits sweet spot between automation and customization

• Automated, versioned mining of GenBank data

• Custom taxonomy tailored for ferns

• Input from taxonomic experts and broader community

• Model for other plant groups at similar scale?

Future directions

• Completion of FTOL

  • “Unlock the vault” of herbarium specimens via plastome skimming

• Integration with Pteridophyte Phylogeny Group II

• Transition to phylogenomics for all species

Acknowledgements

• Japan Society for the Promotion of Science

• Smithsonian National Museum of Natural History Peter Buck Fellowship

• Members of the Iwasaki lab, The University of Tokyo

• A.E. White

• S. Fawcett

• M. Hassler