Earlier this year in January I reported in a CEG blog contribution about tree (or tree-like) ferns, a holiday discovery during a visit to the Adelaide Botanic Garden located in the capital of South Australia. The visit had inspired me to learn more about the biology of this fascinating arborescent (tree-like) plants. I was, thus, very happy when I recently found a scientific article by Zuoying Wei and co-workers published in the prestigious journal Molecular Biology and Evolution that addressed the question how it was possible that tree ferns changed very little in their appearance for more than 100 million years, a phenomenon that researchers refer to as morphological stasis.

Ferns represent one of the oldest lineage of vascular plants that we still find today. They are expected to have originated some 360 million years ago. Among them, we find lineages that remained morphologically almost unchanged (morphological stasis), and were, therefore, often considered as ‘living fossils’. Key questions for evolutionary biologists are how such morphologically static lineages could persist for such long time spans and if morphological stasis reflects genomic stasis as well? Reports of highly conserved karyotypes and very low nucleotide substitution rates may indicate so (Soltis et al., 2002). However, more recent studies on other, morphologically more divers fern lineages revealed considerable indications of dynamic genome evolution (Schneider et al. 2015). No doubt, to more comprehensively understand the stasis-dynamism paradox in ferns more genome data are needed, preferentially from absence closely related fern lineages with different ecological preferences. But to generate such additional data is in technical terms somewhat challenging because ferns tend to have high chromosome numbers (up to 760) and large genomes (up to 160 Gigabases) (Fernandez et al., 2024).

Tree fern species that we find today belong mostly to the family Cyatheaceae (scaly tree ferns) within the order Cyatheales that traces back to the Early Jurassic (some 201 – 174 million years ago). The family Cyatheaceae, however, is expected to date back to the Late Jurassic (some 161 – 145 million years ago). Despite the evolutionary success and ecological adaptation Cyatheaceae has experienced exceptionally low diversification rates over the past 145 million years.

Wei and co-workers now sequenced and assembled the genomes of three further fern species from the same family (Cyatheaceae) that differ in morphology and habitat ecology. They were:
– Sphaeropteris brunoniana (no well established common name), an arborescent tree fern that is distributed in the subtropical regions of North-East Nepal and China to Indo-China. The species can grow 10-20 meters high.
– Gymnosphaera denticulata (stump-footed fern), an up to 4 meters high, non-arborescent species found at elevations >600m in Japan, the islands of the East China Sea down to Hainan as well as the mainland of East China.
– Sphaeropteris lepifera (brush pot tree), also an arborescent species that can grow up to about 6 meters high. It is distributed in mountainous regions of East and Southeast Asia as well as being reported from Central America.

When Wei and coworkers then analyzed the obtained genomic data along with the recently sequenced genome of the up to 5 meters high flying spider-monkey tree fern Alsophila spinulosa (Huang et al., 2022) they inferred support for a whole genome duplication event that dated back to the Jurassic some 154 million years ago. Such whole genome duplication are known to offer the potential for further adaptive evolution, and their role in speciation of ferns has also been discussed (Wood et al., 2009). More detailed analyses by Wei and colleagues also indicated that fern lineages that led to the tree-like S. brunoniana and S. lepifera retained after the whole genome duplication duplicated genes with a function involved in cell wall biogenesis that strengthened structural reinforcement and lignification. In the non-arborescent G. denticulata they found conserved duplicated genes linked to metabolic resilience and defense. In short, there were indications for genomic innovation in the context of morphological stasis, and Wei and coworkers conclude that their findings resolve the stasis-dynamism paradox in tree ferns by regulated genomic innovation rather than static genome architecture.

These results are also in line with the potential of ferns for hybridization that is discussed in a previous CEG-blog post of this year’s advent calendar by Thomas Marcussen where he discusses that horsetail (Equisetum) fern species still hybridise roughly 100 million years since they diverged.

References and further reading:

Fernández P., Amice R., Bruy D., Christenhusz M.J.M., Leitch I.J., Leitch A.L., Pokorny L., Hidalgo O., Pellicer J. 2024. A 160 Gbp fork fern genome shatters size record for eukaryotes.
iScience 27: 109889. https://doi.org/10.1016/j.isci.2024.109889.

Huang X., Wan, W., Gong T. et al. 2022. The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence. Nature Plants 8: 500–512. https://doi.org/10.1038/s41477-022-01146-6

Schneider H., Liu H., Clark J., Hidalgo O., Pellicer J., Zhang S., Kelly L.J., Fay M.F., Leitch I.J. 2015. Are the genomes of royal ferns really frozen in time? Evidence for coinciding genome stability and limited evolvability in the royal ferns. New Phytologist 207: 10–13. https://doi.org/10.1111/nph.13330

Soltis P.S., Soltis D.E., Savolainen V., Crane P.R., Barraclough T.G. 2002. Rate heterogeneity among lineages of tracheophytes: integration of molecular and fossil data and evidence for molecular living fossils. Proceedings of the National Academy of Sciences USA 99: 4430–4435. https://doi.org/10.1073/pnas.032087199

Wei Z., Chen H., Chao Feng, Xia Z., Van de Peer Y., Kang M., Wang J. 2025. Resolving the Stasis-Dynamism Paradox: Genome Evolution in Tree Ferns. Molecular Biology and Evolution 42: msaf247. https://doi.org/10.1093/molbev/msaf247

Wood, T.E., Takebayashi, N., Barker, M.S., Mayrose, I., Greenspoon, P.B. & Rieseberg, L.H. 2009. The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences of the United States of America 106: 13875–13879.
https://doi.org/10.1073/pnas.0811575106

Earlier CEG blog posts on the topic:
Lutz Bachmann – Group of the Month: Tree ferns – an Australian holiday discovery
https://blog.annelida.de/2025/01/23/group-of-the-month-tree-ferns-an-australian-holiday-discovery/
Thomas Marcussen – Door 5: Horsetail (Equisetum) species still hybridise, 100 million years after they diverged
https://blog.annelida.de/2025/12/05/door-5-horsetail-equisetum-species-still-hybridise-100-million-years-after-they-diverged/