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Hori K. Athyrium bipinnatum K.Hori (Athyriaceae), a new cornopteroid fern from Japan. PHYTOKEYS 2020; 148:93-104. [PMID: 32536786 PMCID: PMC7270079 DOI: 10.3897/phytokeys.148.51589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
I describe Athyrium bipinnatum sp. nov. and discuss morphological differences between closely related species. The new species is endemic to Japan, occurring on the islands of Honshu, Kyushu, and Shikoku. Based on the criteria of the International union for conservation of nature and natural resources, this new species is here considered endangered.
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Affiliation(s)
- Kiyotaka Hori
- The Kochi Prefectural Makino Botanical Garden, Kochi, JapanKochi Prefectural Makino Botanical GardenKochiJapan
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2
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Wei R, Zhang XC. Phylogeny of Diplazium (Athyriaceae) revisited: Resolving the backbone relationships based on plastid genomes and phylogenetic tree space analysis. Mol Phylogenet Evol 2019; 143:106699. [PMID: 31809851 DOI: 10.1016/j.ympev.2019.106699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/01/2019] [Accepted: 12/01/2019] [Indexed: 11/17/2022]
Abstract
Despite progress in resolving the phylogeny of twinsorus ferns (Diplazium) based on multilocus phylogenetic studies, uncertainty remains especially for deep, or backbone relationships among closely related clades, suggesting a classic case of rapid evolutionary radiation. Here, we investigated the deep phylogenetic relationships within Diplazium by sampling all major clades and using 51 plastid genomes (plastomes), of which 38 were newly sequenced with high-throughput sequencing technology, resulting more than 127,000 informative sites. Using parsimony, maximum likelihood and Bayesian analyses of plastome sequences, we largely resolved the backbone of the phylogeny of Diplazium with strong support. However, we also detected phylogenetic incongruence among different datasets and moderately to poorly supported relationships, particularly at several extremely short internal branches. By using phylogenetic tree space and topology-clustering analyses, we provide evidence that conflicting phylogenetic signals can be found across the trees estimated from individual chloroplast protein-coding genes, which may underlie the difficulty of systematics of Diplazium. Furthermore, our phylogenetic estimate offers more resolution over previous multilocus analyses, providing a framework for future taxonomic revisions of sectional classification of Diplazium. Our study demonstrates the advantage of a character-rich plastome dataset, combining the comparison of different phylogenetic methods, for resolving the recalcitrant lineages that have undergone rapid radiation and dramatic changes in evolutionary rates.
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Affiliation(s)
- Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China.
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3
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Comparative phylogenetics of some species of Ophioglossum L. (Ophioglossaceae: Pteridophyta) in India with comments on evolutionary significance of high palaeoploidy and rare morphological traits. THE NUCLEUS 2019. [DOI: 10.1007/s13237-019-00287-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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4
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Wei R, Yan YH, Harris AJ, Kang JS, Shen H, Xiang QP, Zhang XC. Plastid Phylogenomics Resolve Deep Relationships among Eupolypod II Ferns with Rapid Radiation and Rate Heterogeneity. Genome Biol Evol 2018; 9:1646-1657. [PMID: 28854625 PMCID: PMC5534337 DOI: 10.1093/gbe/evx107] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2017] [Indexed: 01/21/2023] Open
Abstract
The eupolypods II ferns represent a classic case of evolutionary radiation and, simultaneously, exhibit high substitution rate heterogeneity. These factors have been proposed to contribute to the contentious resolutions among clades within this fern group in multilocus phylogenetic studies. We investigated the deep phylogenetic relationships of eupolypod II ferns by sampling all major families and using 40 plastid genomes, or plastomes, of which 33 were newly sequenced with next-generation sequencing technology. We performed model-based analyses to evaluate the diversity of molecular evolutionary rates for these ferns. Our plastome data, with more than 26,000 informative characters, yielded good resolution for deep relationships within eupolypods II and unambiguously clarified the position of Rhachidosoraceae and the monophyly of Athyriaceae. Results of rate heterogeneity analysis revealed approximately 33 significant rate shifts in eupolypod II ferns, with the most heterogeneous rates (both accelerations and decelerations) occurring in two phylogenetically difficult lineages, that is, the Rhachidosoraceae–Aspleniaceae and Athyriaceae clades. These observations support the hypothesis that rate heterogeneity has previously constrained the deep phylogenetic resolution in eupolypods II. According to the plastome data, we propose that 14 chloroplast markers are particularly phylogenetically informative for eupolypods II both at the familial and generic levels. Our study demonstrates the power of a character-rich plastome data set and high-throughput sequencing for resolving the recalcitrant lineages, which have undergone rapid evolutionary radiation and dramatic changes in substitution rates.
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Affiliation(s)
- Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China
| | - Yue-Hong Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, P.R. China
| | - A J Harris
- Department of Botany, Smithsonian Institution, National Museum of Natural History, Washington, District of Columbia
| | - Jong-Soo Kang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China.,University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hui Shen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Qiao-Ping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China
| | - Xian-Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, P.R. China
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Wei R, Ebihara A, Zhu YM, Zhao CF, Hennequin S, Zhang XC. A total-evidence phylogeny of the lady fern genus Athyrium Roth (Athyriaceae) with a new infrageneric classification. Mol Phylogenet Evol 2018; 119:25-36. [DOI: 10.1016/j.ympev.2017.10.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/17/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022]
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6
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Kuo LY, Ebihara A, Kato M, Rouhan G, Ranker TA, Wang CN, Chiou WL. Morphological characterization of infra-generic lineages inDeparia(Athyriaceae: Polypodiales). Cladistics 2017; 34:78-92. [DOI: 10.1111/cla.12192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2017] [Indexed: 12/21/2022] Open
Affiliation(s)
- Li-Yaung Kuo
- Institute of Ecology and Evolutionary Biology; National Taiwan University; Taipei 10617 Taiwan
| | - Atsushi Ebihara
- Department of Botany; National Museum of Nature and Science; Amakubo 4-1-1 Tsukuba Ibaraki 305-0005 Japan
| | - Masahiro Kato
- Department of Botany; National Museum of Nature and Science; Amakubo 4-1-1 Tsukuba Ibaraki 305-0005 Japan
| | - Germinal Rouhan
- Muséum National d'Histoire Naturelle; Institut de Systématique, Evolution, Biodiversité (UMR 7205 CNRS, MNHN, UPMC, EPHE); Herbier national; 16 rue Buffon CP39 Paris F-75005 France
| | - Tom A. Ranker
- Department of Botany; University of Hawai'i at Mānoa; Honolulu HI 96822 USA
| | - Chun-Neng Wang
- Institute of Ecology and Evolutionary Biology; National Taiwan University; Taipei 10617 Taiwan
- Department of Life Science; National Taiwan University; Taipei 10617 Taiwan
| | - Wen-Liang Chiou
- Taiwan Forestry Research Institute; Taipei 10066 Taiwan
- Dr. Cecilia Koo Botanic Conservation Center; Pingtung County 906 Taiwan
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Kuo LY, Ebihara A, Shinohara W, Rouhan G, Wood KR, Wang CN, Chiou WL. Historical biogeography of the fern genus Deparia (Athyriaceae) and its relation with polyploidy. Mol Phylogenet Evol 2016; 104:123-134. [DOI: 10.1016/j.ympev.2016.08.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 08/06/2016] [Accepted: 08/09/2016] [Indexed: 12/14/2022]
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Shao Y, Wei R, Zhang X, Xiang Q. Molecular Phylogeny of the Cliff Ferns (Woodsiaceae: Polypodiales) with a Proposed Infrageneric Classification. PLoS One 2015; 10:e0136318. [PMID: 26348852 PMCID: PMC4562699 DOI: 10.1371/journal.pone.0136318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 08/01/2015] [Indexed: 11/30/2022] Open
Abstract
The cliff fern family Woodsiaceae has experienced frequent taxonomic changes at the familial and generic ranks since its establishment. The bulk of its species were placed in Woodsia, while Cheilanthopsis, Hymenocystis, Physematium, and Protowoodsia are segregates recognized by some authors. Phylogenetic relationships among the genera of Woodsiaceae remain unclear because of the extreme morphological diversity and inadequate taxon sampling in phylogenetic studies to date. In this study, we carry out comprehensive phylogenetic analyses of Woodsiaceae using molecular evidence from four chloroplast DNA markers (atpA, matK, rbcL and trnL–F) and covering over half the currently recognized species. Our results show three main clades in Woodsiaceae corresponding to Physematium (clade I), Cheilanthopsis–Protowoodsia (clade II) and Woodsia s.s. (clade III). In the interest of preserving monophyly and taxonomic stability, a broadly defined Woodsia including the other segregates is proposed, which is characterized by the distinctive indument and inferior indusia. Therefore, we present a new subgeneric classification of the redefined Woodsia based on phylogenetic and ancestral state reconstructions to better reflect the morphological variation, geographic distribution pattern, and evolutionary history of the genus. Our analyses of the cytological character evolution support multiple aneuploidy events that have resulted in the reduction of chromosome base number from 41 to 33, 37, 38, 39 and 40 during the evolutionary history of the cliff ferns.
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Affiliation(s)
- Yizhen Shao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qiaoping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- * E-mail:
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Sundue MA, Rothfels CJ. Stasis and convergence characterize morphological evolution in eupolypod II ferns. ANNALS OF BOTANY 2014; 113:35-54. [PMID: 24197753 PMCID: PMC3864719 DOI: 10.1093/aob/mct247] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/03/2013] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS Patterns of morphological evolution at levels above family rank remain underexplored in the ferns. The present study seeks to address this gap through analysis of 79 morphological characters for 81 taxa, including representatives of all ten families of eupolypod II ferns. Recent molecular phylogenetic studies demonstrate that the evolution of the large eupolypod II clade (which includes nearly one-third of extant fern species) features unexpected patterns. The traditional 'athyrioid' ferns are scattered across the phylogeny despite their apparent morphological cohesiveness, and mixed among these seemingly conservative taxa are morphologically dissimilar groups that lack any obvious features uniting them with their relatives. Maximum-likelihood and maximum-parsimony character optimizations are used to determine characters that unite the seemingly disparate groups, and to test whether the polyphyly of the traditional athyrioid ferns is due to evolutionary stasis (symplesiomorphy) or convergent evolution. The major events in eupolypod II character evolution are reviewed, and character and character state concepts are reappraised, as a basis for further inquiries into fern morphology. METHODS Characters were scored from the literature, live plants and herbarium specimens, and optimized using maximum-parsimony and maximum-likelihood, onto a highly supported topology derived from maximum-likelihood and Bayesian analysis of molecular data. Phylogenetic signal of characters were tested for using randomization methods and fitdiscrete. KEY RESULTS The majority of character state changes within the eupolypod II phylogeny occur at the family level or above. Relative branch lengths for the morphological data resemble those from molecular data and fit an ancient rapid radiation model (long branches subtended by very short backbone internodes), with few characters uniting the morphologically disparate clades. The traditional athyrioid ferns were circumscribed based upon a combination of symplesiomorphic and homoplastic characters. Petiole vasculature consisting of two bundles is ancestral for eupolypods II and a synapomorphy for eupolypods II under deltran optimization. Sori restricted to one side of the vein defines the recently recognized clade comprising Rhachidosoraceae through Aspleniaceae, and sori present on both sides of the vein is a synapomorphy for the Athyriaceae sensu stricto. The results indicate that a chromosome base number of x =41 is synapomorphic for all eupolypods, a clade that includes over two-thirds of extant fern species. CONCLUSIONS The integrated approach synthesizes morphological studies with current phylogenetic hypotheses and provides explicit statements of character evolution in the eupolypod II fern families. Strong character support is found for previously recognized clades, whereas few characters support previously unrecognized clades. Sorus position appears to be less complicated than previously hypothesized, and linear sori restricted to one side of the vein support the clade comprising Aspleniaceae, Diplaziopsidaceae, Hemidictyaceae and Rachidosoraceae - a lineage only recently identified. Despite x =41 being a frequent number among extant species, to our knowledge it has not previously been demonstrated as the ancestral state. This is the first synapomorphy proposed for the eupolypod clade, a lineage comprising 67 % of extant fern species. This study provides some of the first hypotheses of character evolution at the family level and above in light of recent phylogenetic results, and promotes further study in an area that remains open for original observation.
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Affiliation(s)
- Michael A. Sundue
- The Pringle Herbarium, Department of Plant Biology, University of Vermont, Burlington, VT 05401, USA
| | - Carl J. Rothfels
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
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10
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Rothfels CJ, Larsson A, Li FW, Sigel EM, Huiet L, Burge DO, Ruhsam M, Graham SW, Stevenson DW, Wong GKS, Korall P, Pryer KM. Transcriptome-mining for single-copy nuclear markers in ferns. PLoS One 2013; 8:e76957. [PMID: 24116189 PMCID: PMC3792871 DOI: 10.1371/journal.pone.0076957] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/27/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Molecular phylogenetic investigations have revolutionized our understanding of the evolutionary history of ferns-the second-most species-rich major group of vascular plants, and the sister clade to seed plants. The general absence of genomic resources available for this important group of plants, however, has resulted in the strong dependence of these studies on plastid data; nuclear or mitochondrial data have been rarely used. In this study, we utilize transcriptome data to design primers for nuclear markers for use in studies of fern evolutionary biology, and demonstrate the utility of these markers across the largest order of ferns, the Polypodiales. PRINCIPAL FINDINGS We present 20 novel single-copy nuclear regions, across 10 distinct protein-coding genes: ApPEFP_C, cryptochrome 2, cryptochrome 4, DET1, gapCpSh, IBR3, pgiC, SQD1, TPLATE, and transducin. These loci, individually and in combination, show strong resolving power across the Polypodiales phylogeny, and are readily amplified and sequenced from our genomic DNA test set (from 15 diploid Polypodiales species). For each region, we also present transcriptome alignments of the focal locus and related paralogs-curated broadly across ferns-that will allow researchers to develop their own primer sets for fern taxa outside of the Polypodiales. Analyses of sequence data generated from our genomic DNA test set reveal strong effects of partitioning schemes on support levels and, to a much lesser extent, on topology. A model partitioned by codon position is strongly favored, and analyses of the combined data yield a Polypodiales phylogeny that is well-supported and consistent with earlier studies of this group. CONCLUSIONS The 20 single-copy regions presented here more than triple the single-copy nuclear regions available for use in ferns. They provide a much-needed opportunity to assess plastid-derived hypotheses of relationships within the ferns, and increase our capacity to explore aspects of fern evolution previously unavailable to scientific investigation.
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Affiliation(s)
- Carl J. Rothfels
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Erin M. Sigel
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Dylan O. Burge
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Gane Ka-Shu Wong
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Kathleen M. Pryer
- Department of Biology, Duke University, Durham, North Carolina, United States of America
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11
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Rothfels CJ, Larsson A, Kuo LY, Korall P, Chiou WL, Pryer KM. Overcoming Deep Roots, Fast Rates, and Short Internodes to Resolve the Ancient Rapid Radiation of Eupolypod II Ferns. Syst Biol 2012; 61:490-509. [DOI: 10.1093/sysbio/sys001] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Carl J. Rothfels
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
| | - Anders Larsson
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Li-Yaung Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Petra Korall
- Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Wen-Liang Chiou
- Botanical Garden Division, Taiwan Forestry Research Institute, 53 Nan-hai Road, Taipei 10066, Taiwan
| | - Kathleen M. Pryer
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
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12
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Abstract
In the past two decades, molecular systematic studies have revolutionized our understanding of the evolutionary history of ferns. The availability of large molecular data sets together with efficient computer algorithms, now enables us to reconstruct evolutionary histories with previously unseen completeness. Here, the most comprehensive fern phylogeny to date, representing over one-fifth of the extant global fern diversity, is inferred based on four plastid genes. Parsimony and maximum-likelihood analyses provided a mostly congruent results and in general supported the prevailing view on the higher-level fern systematics. At a deep phylogenetic level, the position of horsetails depended on the optimality criteria chosen, with horsetails positioned as the sister group either of Marattiopsida-Polypodiopsida clade or of the Polypodiopsida. The analyses demonstrate the power of using a 'supermatrix' approach to resolve large-scale phylogenies and reveal questionable taxonomies. These results provide a valuable background for future research on fern systematics, ecology, biogeography and other evolutionary studies.
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13
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Kuo LY, Li FW, Chiou WL, Wang CN. First insights into fern matK phylogeny. Mol Phylogenet Evol 2011; 59:556-66. [DOI: 10.1016/j.ympev.2011.03.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 02/19/2011] [Accepted: 03/05/2011] [Indexed: 10/18/2022]
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Liu H, Zhang X, Chen Z, Qiu Y. Inclusion of the Eastern Asia endemic genus Sorolepidium in Polystichum (Dryopteridaceae): Evidence from the chloroplast rbcL gene and morphological characteristics. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11434-007-0115-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Small RL, Lickey EB, Shaw J, Hauk WD. Amplification of noncoding chloroplast DNA for phylogenetic studies in lycophytes and monilophytes with a comparative example of relative phylogenetic utility from Ophioglossaceae. Mol Phylogenet Evol 2005; 36:509-22. [PMID: 15935702 DOI: 10.1016/j.ympev.2005.04.018] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2004] [Revised: 04/06/2005] [Accepted: 04/20/2005] [Indexed: 11/19/2022]
Abstract
Noncoding DNA sequences from numerous regions of the chloroplast genome have provided a significant source of characters for phylogenetic studies in seed plants. In lycophytes and monilophytes (leptosporangiate ferns, eusporangiate ferns, Psilotaceae, and Equisetaceae), on the other hand, relatively few noncoding chloroplast DNA regions have been explored. We screened 30 lycophyte and monilophyte species to determine the potential utility of PCR amplification primers for 18 noncoding chloroplast DNA regions that have previously been used in seed plant studies. Of these primer sets eight appear to be nearly universally capable of amplifying lycophyte and monilophyte DNAs, and an additional six are useful in at least some groups. To further explore the application of noncoding chloroplast DNA, we analyzed the relative phylogenetic utility of five cpDNA regions for resolving relationships in Botrychium s.l. (Ophioglossaceae). Previous studies have evaluated both the gene rbcL and the trnL(UAA)-trnF(GAA) intergenic spacer in this group. To these published data we added sequences of the trnS(GCU)-trnG(UUC) intergenic spacer + the trnG(UUC) intron region, the trnS(GGA)-rpS4 intergenic spacer+rpS4 gene, and the rpL16 intron. Both the trnS(GCU)-trnG(UUC) and rpL16 regions are highly variable in angiosperms and the trnS(GGA)-rpS4 region has been widely used in monilophyte phylogenetic studies. Phylogenetic resolution was equivalent across regions, but the strength of support for the phylogenies varied among regions. Of the five sampled regions the trnS(GCU)-trnG(UUC) spacer+trnG(UUC) intron region provided the strongest support for the inferred phylogeny.
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Affiliation(s)
- Randall L Small
- Department of Ecology and Evolutionary Biology, The University of Tennessee, Knoxville, TN 37996, USA.
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16
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Lu JM, Li DZ, Gao LM, Cheng X, Wu D. Paraphyly of Cyrtomium (Dryopteridaceae): evidence from rbcL and trnL-F sequence data. JOURNAL OF PLANT RESEARCH 2005; 118:129-135. [PMID: 15818470 DOI: 10.1007/s10265-005-0201-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2004] [Accepted: 02/03/2005] [Indexed: 05/24/2023]
Abstract
Cyrtomium is an Asiatic genus characterized by anastomosing veins with included veinlets, and comprises about 40 species. We sequenced rbcL and trnL-F sequences of 19 species of Cyrtomium and eight species from related genera in order to elucidate a molecular phylogeny of the genus using maximum-parsimony methods. The phylogenetic trees did not agree with traditional classifications. Cyrtomium was resolved as paraphyletic, and a clade including subseries Balansana of Cyrtomium, Cyrtogonellum, Polystichum subacutidens and Cyrtomidictyum (the BCPC clade) and a second one containing Cyrtomium sensu stricto were monophyletic. The results also implied that: (1) C. uniseriale was synonymous with C. balansae; (2) C. falcatum was likely the female parent of C. devexiscapulae; and (3) based on the rbcL and trnL-F sequence data, C. nephrolepioides and C. grossum were the female parents of C. shingianum and C. chingianum, respectively, although other evidence is needed for the confirmation of this hypothesis.
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Affiliation(s)
- Jin-Mei Lu
- Laboratory of Plant Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Heilongtan, Kunming, Yunnan Province, 650204, People's Republic of China
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Rouhan G, Dubuisson JY, Rakotondrainibe F, Motley TJ, Mickel JT, Labat JN, Moran RC. Molecular phylogeny of the fern genus Elaphoglossum (Elaphoglossaceae) based on chloroplast non-coding DNA sequences: contributions of species from the Indian Ocean area. Mol Phylogenet Evol 2004; 33:745-63. [PMID: 15522801 DOI: 10.1016/j.ympev.2004.08.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Revised: 05/12/2004] [Indexed: 11/25/2022]
Abstract
We performed a phylogenetic analysis of the fern genus Elaphoglossum using two non-coding chloroplast spacers: trnL-trnF and rps4-trnS. The sampling includes 123 species, of which 80 have not been previously sequenced, and for the first time includes species from Africa and the Indian Ocean area. The results of this expanded study largely agree with an earlier molecular study based on a smaller group of neotropical species and with the morphology-based classification of Mickel and Atehortua. We found, however, that some infrageneric groups such as section Elaphoglossum are not monophyletic. Besides section Elaphoglossum pro parte, we recognize six sections: two new monospecific, unnamed sections, and the previously established sections Lepidoglossa, Squamipedia, Amygdalifolia, and "Subulate-scaled clade." We divide the subulate-scaled clade into subsection Setosa (hydathodes present) and Polytrichia (hydathodes absent), and section Elaphoglossum is divided into subsections Platyglossa and Pachyglossa, two groups that do not appear to be supported by any single morphological character. In general, however, the main clades are supported by morphology. Finally, we discuss the species of the Indian Ocean region and their affinities with the neotropical ones. Out of the 11 species pairs postulated by Moran and Smith on the basis of morphology, two are well supported (E. eximium-E. aubertii; E. piloselloides-E. spatulatum) and three are not supported (E. ciliatum-E. humbertii; E. muscosum-E. poolii; E. paleaceum-E. deckenii), and two remain unresolved (E. erinaceum-E. hybridum; E. glabellum-E. acrostichoides) because our molecular markers were not variable enough. Four species pairs could not be tested because specimens were lacking. Unsupported species pairs are best interpreted as morphological convergences. Two additional species pairs are proposed: E. cuspidatum-E. succisaefolium; E. doanense-E. hornei. Placement of the species from the Indian Ocean suggests that at least 13 long-distance dispersal events occurred between the Neotropics and the Indian Ocean-Africa.
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Affiliation(s)
- Germinal Rouhan
- Département Systématique et Evolution USM 602, Herbier National Plantes Vasculaires, Muséum National d'Histoire Naturelle, 16 rue Buffon, 75005 Paris, France.
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Hauk WD, Parks CR, Chase MW. Phylogenetic studies of Ophioglossaceae: evidence from rbcL and trnL-F plastid DNA sequences and morphology. Mol Phylogenet Evol 2003; 28:131-51. [PMID: 12801476 DOI: 10.1016/s1055-7903(03)00032-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Ophioglossaceae are a putatively ancient lineage of ferns in which the aerial portion of the plant is composed of a single leaf. The simplicity of foliar morphology has limited the number of characters available for constructing classifications and contributed to taxonomic difficulties at nearly every level of classification within the family. Analysis of plastid DNA rbcL sequences from 36 species representing the diversity of Ophioglossaceae supported the monophyly of the family. Intrafamilial relationships were examined using rbcL and trnL-F plastid DNA sequences and morphological data. Individual and combined analyses of the three data sets revealed two main clades within the family, here termed ophioglossoid and botrychioid. In the botrychioid clade, Helminthostachys was sister to a broadly defined Botrychium, within which Botrychium in the narrow sense of some authors and Sceptridium were sister. Botrypus was paraphyletic, with Botrypus virginianus sister to Botrychium plus Sceptridium, and with Botrypus strictus sister to all other botrychioid species except Helminthostachys. In the ophioglossoid clade, Ophioglossum in the narrow sense was sister to Cheiroglossa plus Ophioderma, but relationships within Ophioglossum were not well supported.
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Affiliation(s)
- Warren D Hauk
- University of North Carolina, Chapel Hill, NC 27516, USA.
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Katoh H, Shiga Y, Nakahira Y, Ohmori M. Isolation and Characterization of a Drought-Tolerant Cyanobacterium, Nostoc sp. HK-01. Microbes Environ 2003. [DOI: 10.1264/jsme2.18.82] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Hiroshi Katoh
- Department of Life Sciences (Biology), University of Tokyo
| | - Yoko Shiga
- Department of Life Sciences (Biology), University of Tokyo
| | - Yuka Nakahira
- Department of Life Sciences (Biology), University of Tokyo
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