Methods – Fern Tree of Life

For a full description of methods, see Nitta et al. (2022).

The goal of this project is to produce a maximally sampled global fern phylogeny.

All DNA sequence data were downloaded from GenBank. The current FTOL (v1.7.0) includes sequences up to 2024-06-15 (GenBank release 261).

Input data, including a database containing fern sequences from GenBank release 261, are available on FigShare.

Two datasets were produced:

The “plastome” dataset includes 79 loci obtained from whole plastomes for 654 species (including outgroup taxa).
The “Sanger” dataset includes 7 plastid loci for 5,869 species (including outgroup taxa).

Phylogenetic analysis was carried out using maximum likelihood in IQ-TREE (Nguyen et al. 2015) in two steps. First, a backbone phylogeny was built using the plastome dataset. Next, the full phylogeny was built using the Sanger dataset with the backbone phylogeny as a constraint tree. For both analyses, all loci were concatenated and no partitioning was used.

The tree was dated using treePL (Smith and O’Meara 2012) with a set of 54 fossil constraints (not including the root).

References

Nguyen, Lam-Tung, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh. 2015. “IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies.” Molecular Biology and Evolution 32 (1): 268–74. https://doi.org/10.1093/molbev/msu300.

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.

Smith, Stephen A, and Brian C. O’Meara. 2012. “treePL: Divergence Time Estimation Using Penalized Likelihood for Large Phylogenies.” Bioinformatics 28 (20): 2689–90. https://doi.org/10.1093/bioinformatics/bts492.