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Jiang LJ, Zhao J, Wang JG, Landrein S, Shi JP, Huang CJ, Luo M, Zhou XM, Niu HB, He ZR. Deciphering the evolution and biogeography of Ant-ferns Lecanopteris s.s. Mol Phylogenet Evol 2024:108199. [PMID: 39278383 DOI: 10.1016/j.ympev.2024.108199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 09/03/2024] [Accepted: 09/11/2024] [Indexed: 09/18/2024]
Abstract
Southeast Asia is a biodiversity hotspot characterized by a complex paleogeography, and its Polypodiopsida flora is particularly diverse. While hybridization is recognized as common in ferns, further research is needed to investigate the relationship between hybridization events and fern diversity. Lecanopteris s.s., an ant-associated fern, has been subject to debate regarding species delimitations primarily due to limited DNA markers and species sampling. Our study integrates 22 newly generated plastomes, 22 transcriptomes, and flow cytometry of all native species along with two cultivated hybrids. Our objective is to elucidate the reticulate evolutionary history within Lecanopteris s.s. through the integration of phylobiogeographic reconstruction, gene flow inference, and genome size estimation. Key findings of our study include: (1) An enlarged plastome size (178-187 Kb) in Lecanopteris, attributed to extreme expansion of the Inverted Repeat (IR) regions; (2) The traditional 'pumila' and 'crustacea' groups are paraphyletic; (3) Significant cytonuclear discordance attributed to gene flow; (4) Natural hybridization and introgression in the 'pumila' and 'darnaedii' groups; (5) L. luzonensis is the maternal parent of L. 'Yellow Tip', with L. pumila suggested as a possible paternal parent; (6) L. 'Tatsuta' is a hybrid between L. luzonensis and L. crustacea; (7) Lecanopteris first diverged during the Neogene and then during the middle Miocene climatic optimum in the Indochina and Sundaic regions. In conclusion, the biogeographic history and speciation of Lecanopteris have been profoundly shaped by past climate changes and geodynamics of Southeast Asia. Dispersals, hybridization and introgression between species act as pivotal factors in the evolutionary trajectory of Lecanopteris. This research provides a robust framework for further exploration and understanding of the complex dynamics driving the diversification and distribution patterns within Polypodiaceae subfamily Microsoroideae.
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Affiliation(s)
- Li-Ju Jiang
- Gardening and Horticulture Centre, Xishuangbanna Tropic Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China
| | - Jing Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China
| | - Jia-Guan Wang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China
| | - Sven Landrein
- Kadoorie Farm and Botanic Garden, Lam Kam Road, Tai Po, New Territories, Hong Kong Special Administrative Region of China
| | - Ji-Pu Shi
- Gardening and Horticulture Centre, Xishuangbanna Tropic Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China
| | - Chuan-Jie Huang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China
| | - Miao Luo
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China
| | - Xin-Mao Zhou
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China.
| | - Hong-Bin Niu
- Gardening and Horticulture Centre, Xishuangbanna Tropic Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China.
| | - Zhao-Rong He
- School of Life Sciences, Yunnan University, East Outer Ring Road, Chenggong District, Kunming 650500, Yunnan, China.
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Zhou XM, Zhang LB. Phylogeny, character evolution, and classification of Selaginellaceae (lycophytes). PLANT DIVERSITY 2023; 45:630-684. [PMID: 38197007 PMCID: PMC10772194 DOI: 10.1016/j.pld.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 01/11/2024]
Abstract
Selaginella is the largest and most taxonomically complex genus in lycophytes. The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes. Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions (74% increase of the earlier largest sampling) representing ca. 300 species to infer a new phylogeny. The evolution of 10 morphological characters is studied in the new phylogenetic context. Our major results include: (1) the nuclear and plastid phylogenies are congruent with each other and combined analysis well resolved and strongly supported the relationships of all but two major clades; (2) the Sinensis group is resolved as sister to S. subg. Pulviniella with strong support in two of the three analyses; (3) most morphological characters are highly homoplasious but some characters alone or combinations of characters well define the major clades in the family; and (4) an infrafamilial classification of Selaginellaceae is proposed and the currently defined Selaginella s.l. is split into seven subfamilies (corresponding to the current six subgenera + the Sinensis group) and 19 genera (the major diagnosable clades) with nine new species-poor genera. We support the conservation of Selaginella with a new type, S. flabellata, to minimize nomenclatural instability. We provide a key to subfamilies and genera, images illustrating their morphology, their morphological and geographical synopses, a list of constituent species, and necessary new combinations. This new classification will hopefully facilitate communication, promote further studies, and help conservation.
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Affiliation(s)
- Xin-Mao Zhou
- School of Ecology and Environmental Science, Yunnan University, Kunming 650504, Yunnan, China
| | - Li-Bing Zhang
- Missouri Botanical Garden, 4344 Shaw Blvd, St. Louis, Missouri 63110, USA; Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, Sichuan, China
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Lu JM, Du XY, Kuo LY, Ebihara A, Perrie LR, Zuo ZY, Shang H, Chang YH, Li DZ. Plastome phylogenomic analysis reveals evolutionary divergences of Polypodiales suborder Dennstaedtiineae. BMC PLANT BIOLOGY 2022; 22:511. [PMID: 36319964 PMCID: PMC9628275 DOI: 10.1186/s12870-022-03886-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Polypodiales suborder Dennstaedtiineae contain a single family Dennstaedtiaceae, eleven genera, and about 270 species, and include some groups that were previously placed in Dennstaedtiaceae, Hypolepidaceae, Monachosoraceae, and Pteridaceae. The classification and phylogenetic relationships among these eleven genera have been poorly understood. To explore the deep relationships within suborder Dennstaedtiineae and estimate the early diversification of this morphologically heterogeneous group, we analyzed complete plastomes of 57 samples representing all eleven genera of suborder Dennstaedtiineae using maximum likelihood and Bayesian inference. RESULTS The phylogenetic relationships of all the lineages in the bracken fern family Dennstaedtiaceae were well resolved with strong support values. All six genera of Hypolepidoideae were recovered as forming a monophyletic group with full support, and Pteridium was fully supported as sister to all the other genera in Hypolepidoideae. Dennstaedtioideae (Dennstaedtia s.l.) fell into four clades with full support: the Microlepia clade, the northern Dennstaedtia clade, the Dennstaedtia globulifera clade, and the Dennstaedtia s.s. clade. Monachosorum was strongly resolved as sister to all the remaining genera of suborder Dennstaedtiineae. Based on the well resolved relationships among genera, the divergence between Monachosorum and other groups of suborder Dennstaedtiineae was estimated to have occurred in the Early Cretaceous, and all extant genera (and clades) in Dennstaedtiineae, were inferred to have diversified since the Late Oligocene. CONCLUSION This study supports reinstating a previously published family Monachosoraceae as a segregate from Dennstaedtiaceae, based on unique morphological evidence, the shady habitat, and the deep evolutionary divergence from its closest relatives.
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Affiliation(s)
- Jin-Mei Lu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China.
| | - Xin-Yu Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan
| | - Leon R Perrie
- Museum of New Zealand Te Papa Tongarewa, Cable Street, Wellington, 6011, New Zealand
| | - Zheng-Yu Zuo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China
| | - Hui Shang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yi-Han Chang
- Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming, 650201, China.
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Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. An open and continuously updated fern tree of life. FRONTIERS IN PLANT SCIENCE 2022; 13:909768. [PMID: 36092417 PMCID: PMC9449725 DOI: 10.3389/fpls.2022.909768] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/12/2022] [Indexed: 05/31/2023]
Abstract
Ferns, with about 12,000 species, are the second most diverse lineage of vascular plants after angiosperms. They have been the subject of numerous molecular phylogenetic studies, resulting in the publication of trees for every major clade and DNA sequences from nearly half of all species. Global fern phylogenies have been published periodically, but as molecular systematics research continues at a rapid pace, these become quickly outdated. Here, we develop a mostly automated, reproducible, open pipeline to generate a continuously updated fern tree of life (FTOL) from DNA sequence data available in GenBank. Our tailored sampling strategy combines whole plastomes (few taxa, many loci) with commonly sequenced plastid regions (many taxa, few loci) to obtain a global, species-level fern phylogeny with high resolution along the backbone and maximal sampling across the tips. We use a curated reference taxonomy to resolve synonyms in general compliance with the community-driven Pteridophyte Phylogeny Group I classification. The current FTOL includes 5,582 species, an increase of ca. 40% relative to the most recently published global fern phylogeny. Using an updated and expanded list of 51 fern fossil constraints, we find estimated ages for most families and deeper clades to be considerably older than earlier studies. FTOL and its accompanying datasets, including the fossil list and taxonomic database, will be updated on a regular basis and are available via a web portal (https://fernphy.github.io) and R packages, enabling immediate access to the most up-to-date, comprehensively sampled fern phylogeny. FTOL will be useful for anyone studying this important group of plants over a wide range of taxonomic scales, from smaller clades to the entire tree. We anticipate FTOL will be particularly relevant for macroecological studies at regional to global scales and will inform future taxonomic systems with the most recent hypothesis of fern phylogeny.
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Affiliation(s)
- Joel H. Nitta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
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Fujiwara T, Khine PK, Hori K, Shin T, Murakami N, Schneider H. Lepisorusmedioximus (Polypodiales, Polypodiaceae), a new species from Shan State of Myanmar. PHYTOKEYS 2022; 201:23-34. [PMID: 36762316 PMCID: PMC9848922 DOI: 10.3897/phytokeys.201.84911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/22/2022] [Indexed: 06/18/2023]
Abstract
A new species of the species-rich fern genus Lepisorus (Polypodiales, Polypodiaceae) has been found to occur in Shan state, Myanmar. Lepisorusmedioximus is described based on morphological characters and phylogenetic evidence. Phylogenetic analyses showed that the specimens of L.medioximus formed a distinct clade nested in the Pseudovittaria clade. The morphological comparison demonstrated that the species is distinct from phylogenetically related species, namely L.elegans, L.contortus, and L.tosaensis, in the morphology of the rhizome scales, size, and shape of the lamina, position of sori, and paraphyses.
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Affiliation(s)
- Tao Fujiwara
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo 192-0397, JapanXishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesMenglunChina
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, ChinaTokyo Metropolitan UniversityTokyoJapan
| | - Phyo Kay Khine
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, ChinaTokyo Metropolitan UniversityTokyoJapan
| | - Kiyotaka Hori
- The Kochi Prefectural Makino Botanical Garden 4200-6 Godaisan, Kochi 781-8125, JapanThe Kochi Prefectural Makino Botanical GardenKochiJapan
| | - Thant Shin
- Forest Research Institute, Yezin, Nay Pyi Taw, MyanmarForest Research InstituteNay Pyi TawMyanmar
| | - Noriaki Murakami
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minami-osawa, Hachioji, Tokyo 192-0397, JapanXishuangbanna Tropical Botanical Garden, Chinese Academy of SciencesMenglunChina
| | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, ChinaTokyo Metropolitan UniversityTokyoJapan
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Zhang L, Zhang LB. Phylogeny, character evolution, and systematics of the fern family Ophioglossaceae based on Sanger sequence data, plastomes, and morphology. Mol Phylogenet Evol 2022; 173:107512. [PMID: 35595007 DOI: 10.1016/j.ympev.2022.107512] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 03/17/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022]
Abstract
Adder's tongue ferns or Ophioglossaceae are best known among evolutionary biologists and botanists for their highest chromosome count of any known organisms, the presence of sporophores, and simple morphology. Previous studies recovered and strongly supported the monophyly of the family and the two multi-generic subfamilies, Botrychioideae and Ophioglossoideae, but the relationships among these and two other subfamilies (Helminthostachyoideae and Mankyuoideae) are not well resolved preventing us from understanding the character evolution. The monophyly of and the relationships in the species-rich genus, Ophioglossum, have not well been understood. In this study, new phylogenetic trees are reconstructed based on four datasets: Sanger sequences of eight plastid markers of 184 accessions, 22 plastomes (12 are new), 29 morphological characters, and combined Sanger and morphological data. Our major results include: (1) the relationships among the four subfamilies are well resolved and strongly supported in Bayesian and parsimony analyses based on plastomes: Mankyua is sister to the rest, followed by Ophioglossoideae which are sister to Helminthostachys + Botrychioideae; (2) Sanger data, plastomes, and combined Sanger and morphological data recovered and strongly supported the monophyly of Ophioglossum in its current circumscription (sensu lato; s.l.) in Bayesian and/or parsimony analyses; (3) within Ophioglossum s.l., four deeply diverged clades are identified and the relationships among the four clades are well resolved; (4) evolution of 34 morphological characters is analyzed in the context of the new phylogeny, among which shape of rhizomes, germination time of spores, shape of early gametophytes, and a number of other characters are found to contain interesting phylogenetic signal; and (5) based on the new phylogeny and character evolution, we propose a new classification of Ophioglossaceae in which the currently circumscribed Ophioglossum is divided into four genera including three new ones: Goswamia, Haukia, and Whittieria considering their molecular, morphological, ecological, and biogeographical distinctiveness.
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Affiliation(s)
- Liang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Yezin, Nay Pyi Taw 05282, Myanmar
| | - Li-Bing Zhang
- Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, Missouri 63110, U.S.AChengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China.
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Wei R, Zhao CF, Xiang QP, Zhang XC. Ellipinema and ×Ellipisorus? Just Lepisorus (Polypodiaceae)! Mol Phylogenet Evol 2021; 161:107176. [PMID: 33866009 DOI: 10.1016/j.ympev.2021.107176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/26/2021] [Accepted: 04/06/2021] [Indexed: 10/21/2022]
Abstract
The establishment of a segregate lepisoroid fern genus Ellipinema was mainly to accommodate the isolated position of Lepisorus jakonensis (Polypodiaceae) recovered in plastid gene tree. Using newly obtained nuclear data, we recovered that Ellipinema and allied genera, such as Lepidomicrosorium, Lemmaphyllum, Neolepisorus, Paragramma, Tricholepidium and Weatherbya are deeply nested within Lepisorus. The nuclear phylogeny showing incongruent phylogenetic placement in comparison with plastid results perhaps indicated ancient hybridization events. The diagnostic morphology characterizing Ellipinema - elliptic scale-like paraphyses, which is shared by all the taxa of sect. Lepisorus and sect. Hymenophyton - falls within the range of continuous variation in the type species Ellipinema jakonense (=Lepisorus jakonensis). Our study, which integrated molecular and morphological data, demonstrates that the segregation of Ellipinema and ×Ellipisorus (= ×Lepinema Li Bing Zhang & Liang Zhang, nom. illeg.) from Lepisorus should be rejected.
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Affiliation(s)
- Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Cun-Feng Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Chen CC, Liu HY, Chen CW, Schneider H, Hyvönen J. On the spore ornamentation of the microsoroid ferns (microsoroideae, polypodiaceae). JOURNAL OF PLANT RESEARCH 2021; 134:55-76. [PMID: 33251557 PMCID: PMC7817562 DOI: 10.1007/s10265-020-01238-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Microsoroideae is the third largest of the six subfamilies of Polypodiaceae, containing over 180 species. These ferns are widely distributed in the tropical and subtropical regions of the Old World and Oceania. We documented the spore ornamentation and integrated these data into the latest phylogenetic hypotheses, including a sampling of 100 taxa representing each of 17 major lineages of microsoroid ferns. This enabled us to reconstruct the ancestral states of the spore morphology. The results show verrucate ornamentation as an ancestral state for Goniophlebieae and Lecanoptereae, globular for Microsoreae, and rugulate surface for Lepisoreae. In addition, spore ornamentation can be used to distinguish certain clades of the microsoroid ferns. Among all five tribes, Lecanoptereae show most diversity in spore surface ornamentation.
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Affiliation(s)
- Chi-Chuan Chen
- Organismal and Evolutionary Biology, Viikki Plant Science Center and Finnish Museum of Natural History (Botany), University of Helsinki, PO Box 7, 00100, Helsinki, FI, Finland
| | - Ho-Yih Liu
- Department of Biological Sciences, National Sun Yat-Sen University, 70 Lien-hai Rd, Kaohsiung, 804, Taiwan
| | | | - Harald Schneider
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Yunnan, China
| | - Jaakko Hyvönen
- Organismal and Evolutionary Biology, Viikki Plant Science Center and Finnish Museum of Natural History (Botany), University of Helsinki, PO Box 7, 00100, Helsinki, FI, Finland.
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