Integrated Biology Journals
JSE

J Syst Evol ›› 2025, Vol. 63 ›› Issue (4): 835-850.DOI: 10.1111/jse.13164

• Research Article • Previous Articles     Next Articles

Phylotranscriptomic analyses reveal the reticulate evolution in Dennstaedtiaceae

Zeng‐Qiang Xia1,2,3, Ting Wang2, Hui Shang1, Zuo‐Ying Wei2, Quan Yuan1, Li‐Yun Nie2, Ting‐Zhang Li4,5, Li Liu6, Rui Zhang1, Yue‐Hong Yan1,5, Fa‐Guo Wang2*, and Hui Shen1,6*   

  1. 1Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai 201602, China
    2Guangdong Provincial Key Laboratory of Applied Botany, Chinese Academy of Sciences, Guangzhou 510650, China
    3University of Chinese Academy of Sciences, Beijing 100049, China
    4College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
    5Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
    6CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China

    *Authors for correspondence. Fa‐Guo Wang. E‐mail: wangfg@scbg.ac.cn; Hui Shen. E‐mail: shenhui@cemps.ac.cn
  • Received:2024-05-17 Accepted:2024-12-15 Online:2025-03-18 Published:2025-07-01
  • Supported by:
    This study was supported by the National Natural Science Foundation of China (31370234), Shanghai Landscaping and City Appearance Administrative Bureau of China, Scientific Research Grants (G242409, G142433), and Guangdong Flagship Project of Basic and Applied Basic Research (2023B0303050001).

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Abstract: Dennstaedtiaceae, a heterogeneous family of ferns with 11 genera and about 270 species, has a global distribution. While substantial progress has been made in elucidating the intergeneric relationships within Dennstaedtiaceae, certain nodes, particularly within Hypolepidoideae, remain controversial. To date, no phylogenomic investigation of nuclear genes has been conducted for Dennstaedtiaceae, and the biological processes underlying its complex evolution remain largely unknown. In this study, we generated transcriptome sequences from nine species in Dennstaedtiaceae and combined them with publicly available data sets from 13 species and one outgroup. By utilizing the 23 transcriptomic data sets, representing nine out of the 11 genera in Dennstaedtiaceae, we successfully resolved the intergeneric relationships within the family and established a fundamental phylogenetic framework to investigate its evolutionary history. By combining the analyses of rate-adjusted Ks-based age distributions and phylogenetic reconciliation approaches, we found evidence of at least one round of whole-genome duplication (WGD) that is shared by all Dennstaedtiaceae species prior to their divergence. Extensive gene tree discordance was found across the backbone of Dennstaedtiaceae, with the most significant discordance within Hypolepidoideae. The results of incomplete lineage sorting (ILS) simulation revealed that ILS is a substantial contributor to these conflicts. Evidence from phylogenetic networks and introgression tests indicates the occurrence of gene flow among the clades of Paesia, Hiya, and Histiopteris, potentially explaining the observed cytonuclear discordance in Hypolepidoideae. Our phylotranscriptomic study of Dennstaedtiaceae provides novel insights into its complex reticulate evolutionary history, paving the way for future studies aimed at unraveling the mechanisms underlying its diversification and adaptation.

Key words: gene flow, gene tree discordance, hybridization, phylotranscriptomics, reticulate evolution, systematics, wholegenome duplication.

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