Genome-wide data reveal cryptic diversity and hybridization in a group of tree ferns

Huiqin Yi, Shiyong Dong, Lihua Yang, Jing Wang, Catherine Kidner, Ming Kang*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Discovery of cryptic diversity is essential to understanding both the process of speciation and the conservation of species. Determining species boundaries in fern lineages represents a major challenge due to lack of morphologically diagnostic characters and frequent hybridization. Genomic data has substantially enhanced our understanding of the speciation process, increased the resolution of species delimitation studies, and led to the discovery of cryptic diversity. Here, we employed restriction-site-associated DNA sequencing (RAD-seq) and integrated phylogenomic and population genomic analyses to investigate phylogenetic relationships and evolutionary history of 16 tree ferns with marginate scales (Cyatheaceae) from China and Vietnam. We conducted multiple species delimitation analyses using the multispecies coalescent (MSC) model and novel approaches based on genealogical divergence index (gdi) and isolation by distance (IBD). In addition, we inferred species trees using concatenation and several coalescent-based methods, and assessed hybridization patterns and rate of gene flow across the phylogeny. We obtained highly supported and generally congruent phylogenies inferred from concatenated and summary-coalescent methods, and the monophyly of all currently recognized species were strongly supported. Our results revealed substantial evidence of cryptic diversity in three widely distributed Gymnosphaera species, each of which was composite of two highly structure lineages that may correspond to cryptic species. We found that hybridization was fairly common between not only closely related species, but also distantly related species. Collectively, it appears that scaly tree ferns may contain cryptic diversity and hybridization has played an important role throughout the evolutionary history of this group.

Original languageEnglish
Article number107801
Number of pages43
JournalMolecular phylogenetics and evolution
Publication statusPublished - 22 Apr 2023

Keywords / Materials (for Non-textual outputs)

  • cryptic diversity
  • hybridization
  • phylogeny
  • RAD-seq
  • species delimitation
  • tree fern


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