4.4 Article

Chloroplast phylogenomics resolves key relationships in ferns

期刊

JOURNAL OF SYSTEMATICS AND EVOLUTION
卷 53, 期 5, 页码 448-457

出版社

WILEY
DOI: 10.1111/jse.12180

关键词

chloroplast genome; chloroplast phylogenomics; ferns; phylogenetics; polypods

资金

  1. National Key Basic Research Program of China [2014CB954101]
  2. National Natural Science Foundation of China [31129001]
  3. Applied Fundamental Research Foundation of Yunnan Province [2014GA003, 2014FB168]
  4. Laboratories of Analytical Biology of the Smithsonian Institution
  5. Buck Fellowship program of the National Museum of Natural History, Smithsonian Institution

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Studies on chloroplast genomes of ferns and lycophytes are relatively few in comparison with those on seed plants. Although a basic phylogenetic framework of extant ferns is available, relationships among a few key nodes remain unresolved or poorly supported. The primary objective of this study is to explore the phylogenetic utility of large chloroplast gene data in resolving difficult deep nodes in ferns. We sequenced the chloroplast genomes from Cyrtomium devexiscapulae (Koidz.) Ching (eupolypod I) and Woodwardia unigemmata (Makino) Nakai (eupolypod II), and constructed the phylogeny of ferns based on both 48 genes and 64 genes. The trees based on 48 genes and 64 genes are identical in topology, differing only in support values for four nodes, three of which showed higher support values for the 48-gene dataset. Equisetum L. was resolved as the sister to the Psilotales-Ophioglossales clade, and Equisetales-Psilotales-Ophioglossales clade was sister to the clade of the leptosporangiate and marattioid ferns. The sister relationship between the tree fern clade and polypods was supported by 82% and 100% bootstrap values in the 64-gene and 48-gene trees, respectively. Within polypod ferns, Pteridaceae was sister to the clade of Dennstaedtiaceae and eupolypods with a high support value, and the relationship of Dennstaedtiaceae-eupolypods was strongly supported. With recent parallel advances in the phylogenetics of ferns using nuclear data, chloroplast phylogenomics shows great potential in providing a framework for testing the impact of reticulate evolution in the early evolution of ferns.

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