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Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns.

Hui Shen1,2, Dongmei Jin1,2, Jiang-Ping Shu1,2

  • 1Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, 3888 Chenhua Road, Songjiang, Shanghai 201602, China.

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This study resolves controversial fern relationships using phylogenomics. Key findings include Equisetales sister to other ferns and new insights into fern family evolution.

Keywords:
evolutionmonilophytesphylogenomicsporangiumtranscriptome

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Area of Science:

  • Evolutionary biology
  • Phylogenetics
  • Plant science

Background:

  • Ferns (Filicophyta) originated ~360 million years ago and represent the sister group to seed plants.
  • Despite advances, fern phylogeny remains debated due to conflicting molecular and morphological data.

Purpose of the Study:

  • To establish a robust fern phylogeny using large-scale phylogenomic analysis.
  • To resolve controversial relationships among major fern lineages.

Main Methods:

  • Conducted phylogenomic analysis using high-quality transcriptome sequencing data from 69 fern species.
  • Employed both coalescent-based and concatenation-based methods on nucleotide and amino acid sequences for species tree estimation.

Main Results:

  • Confirmed Equisetales as sister to the remaining ferns; Dennstaedtiaceae as sister to eupolypods.
  • Revealed novel relationships: Marattiaceae sister to Psilotaceae/Ophioglossaceae; Gleicheniaceae/Hymenophyllaceae sister to Dipteridaceae; Aspleniaceae sister to eupolypods II.
  • Identified incongruent placements for six specific fern species.

Conclusions:

  • The study provides a robust backbone phylogeny for ferns, resolving long-standing phylogenetic questions.
  • New evolutionary insights into fern sporangial annulus evolution were proposed based on morphological traits.
  • This phylogeny serves as a foundation for future fern biology and evolutionary research.