Recent advances on phylogenomics of gymnosperms and a new classification - PubMed (original) (raw)
Recent advances on phylogenomics of gymnosperms and a new classification
Yong Yang et al. Plant Divers. 2022.
Abstract
Living gymnosperms comprise four major groups: cycads, Ginkgo, conifers, and gnetophytes. Relationships among/within these lineages have not been fully resolved. Next generation sequencing has made available a large number of sequences, including both plastomes and single-copy nuclear genes, for reconstruction of solid phylogenetic trees. Recent advances in gymnosperm phylogenomic studies have updated our knowledge of gymnosperm systematics. Here, we review major advances of gymnosperm phylogeny over the past 10 years and propose an updated classification of extant gymnosperms. This new classification includes three classes (Cycadopsida, Ginkgoopsida, and Pinopsida), five subclasses (Cycadidae, Ginkgoidae, Cupressidae, Pinidae, and Gnetidae), eight orders (Cycadales, Ginkgoales, Araucariales, Cupressales, Pinales, Ephedrales, Gnetales, and Welwitschiales), 13 families, and 86 genera. We also described six new tribes including Acmopyleae Y. Yang, Austrocedreae Y. Yang, Chamaecyparideae Y. Yang, Microcachrydeae Y. Yang, Papuacedreae Y. Yang, and Prumnopityeae Y. Yang, and made 27 new combinations in the genus Sabina.
Keywords: Classification; Gymnosperms; Morphology; New tribe; Phylogenomics; Taxonomy.
© 2022 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd.
Conflict of interest statement
We declare that we have no conflict of interest.
Figures
Fig. 1
Cladogram displaying phylogenetic relationships among extant gymnosperms. Clade color indicates subclasses. Relationships are basically according to recent gymnosperm phylogenies (Lu et al., 2014; Ran et al., 2018a; Stull et al., 2021), Cupressaceae (Mao et al., 2010, 2012, 2019), Cycadales (Condamine et al., 2015), Pinaceae (Ran et al., 2018b), Podocarpaceae (Chen et al., 2022).
Fig. 2
Distribution of the three new tribes of Podocarpaceae. Pink: Acmopyleae Y. Yang, trib. nov.; Blue: Microcachrydeae Y. Yang, trib. nov.; Orange: Prumnopityeae Y. Yang, trib. nov.
Fig. 3
Distribution map of the three new tribes of Cupressaceae. Pink: Austrocedreae Y. Yang, trib. nov.; Orange Chamaecyparideae Y. Yang, trib. nov.; Blue: Papuacedreae Y. Yang, trib. nov.
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References
- Adams R.P. 2nd edition. Trafford Publishing Co.; Vancouver: 2008. Junipers of the World: the Genus Juniperus.
- Adams R.P. 4nd edition. Trafford Publishing Co.; Bloomington: 2014. Junipers of the World: the Genus Juniperus.
- Brummitt R.K. Report of the nomenclature committee for vascular plants: 59. Taxon. 2007;56:1289–1296.
- Chaw S.M., Zharkikh A., Sung H.M., et al. Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Mol. Biol. Evol. 1997;14:56–68. - PubMed
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