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Xue B, Huang E, Zhao G, Wei R, Song Z, Zhang X, Yao G. 'Out of Africa' origin of the pantropical staghorn fern genus Platycerium (Polypodiaceae) supported by plastid phylogenomics and biogeographical analysis. ANNALS OF BOTANY 2024; 133:697-710. [PMID: 38230804 PMCID: PMC11082476 DOI: 10.1093/aob/mcae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/05/2024] [Indexed: 01/18/2024]
Abstract
BACKGROUND AND AIMS The staghorn fern genus Platycerium is one of the most commonly grown ornamental ferns, and it evolved to occupy a typical pantropical intercontinental disjunction. However, species-level relationships in the genus have not been well resolved, and the spatiotemporal evolutionary history of the genus also needs to be explored. METHODS Plastomes of all the 18 Platycerium species were newly sequenced. Using plastome data, we reconstructed the phylogenetic relationships among Polypodiaceae members with a focus on Platycerium species, and further conducted molecular dating and biogeographical analyses of the genus. KEY RESULTS The present analyses yielded a robustly supported phylogenetic hypothesis of Platycerium. Molecular dating results showed that Platycerium split from its sister genus Hovenkampia ~35.2 million years ago (Ma) near the Eocene-Oligocene boundary and began to diverge ~26.3 Ma during the late Oligocene, while multiple speciation events within Platycerium occurred during the middle to late Miocene. Biogeographical analysis suggested that Platycerium originated in tropical Africa and then dispersed eastward to southeast Asia-Australasia and westward to neotropical areas. CONCLUSIONS Our analyses using a plastid phylogenomic approach improved our understanding of the species-level relationships within Platycerium. The global climate changes of both the Late Oligocene Warming and the cooling following the mid-Miocene Climate Optimum may have promoted the speciation of Platycerium, and transoceanic long-distance dispersal is the most plausible explanation for the pantropical distribution of the genus today. Our study investigating the biogeographical history of Platycerium provides a case study not only for the formation of the pantropical intercontinental disjunction of this fern genus but also the 'out of Africa' origin of plant lineages.
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Affiliation(s)
- Bine Xue
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Erfeng Huang
- Guangxi Nanning Roy Garden Co., Ltd, Nanning 530227, China
| | - Guohua Zhao
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhuqiu Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Gang Yao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
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Testo WL, de Gasper AL, Molino S, Galán JMGY, Salino A, Dittrich VADO, Sessa EB. Deep vicariance and frequent transoceanic dispersal shape the evolutionary history of a globally distributed fern family. AMERICAN JOURNAL OF BOTANY 2022; 109:1579-1595. [PMID: 36063431 DOI: 10.1002/ajb2.16062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The historical biogeography of ferns is typically expected to be dominated by long-distance dispersal due to their minuscule spores. However, few studies have inferred the historical biogeography of a large and widely distributed group of ferns to test this hypothesis. Our aims were to determine the extent to which long-distance dispersal vs. vicariance have shaped the history of the fern family Blechnaceae, to explore ecological correlates of dispersal and diversification, and to determine whether these patterns differ between the northern and southern hemispheres. METHODS We used sequence data for three chloroplast loci to infer a time-calibrated phylogeny for 154 of 265 species of Blechnaceae, including representatives of all genera in the family. This tree was used to conduct ancestral range reconstruction and stochastic character mapping, estimate diversification rates, and identify ecological correlates of diversification. RESULTS Blechnaceae originated in Eurasia and began diversifying in the late Cretaceous. A lineage comprising most extant diversity diversified principally in the austral Pacific region around the Paleocene-Eocene Thermal Maximum. Land connections that existed near the poles during periods of warm climates likely facilitated migration of several lineages, with subsequent climate-mediated vicariance shaping current distributions. Long-distance dispersal is frequent and asymmetrical, with New Zealand/Pacific Islands, Australia, and tropical America being major source areas. CONCLUSIONS Ancient vicariance and extensive long-distance dispersal have shaped the history of Blechnaceae in both the northern and southern hemispheres. The exceptional diversity in austral regions appears to reflect rapid speciation in these areas; mechanisms underlying this evolutionary success remain uncertain.
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Affiliation(s)
- Weston L Testo
- Department of Biology, 876 Newell Drive, University of Florida, Gainesville, FL, 32611, USA
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX, 76102, USA
- Department of Science and Education, Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL, 60605, USA
| | - André L de Gasper
- Departamento de Ciências Naturais, Universidade Regional de Blumenau, Rua Antônio da Veiga, 140, Victor Konder, CEP 89030-903, Blumenau, SC, Brazil
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Federal de Minas Gerais, P.O. Box 486, 31270-901, Belo Horizonte, MG, Brazil
| | - Sonia Molino
- Unit of Botany, Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense, Avda. Jose Antonio Nováis 12, 28040, Madrid, Spain
| | - José María Gabriel Y Galán
- Unit of Botany, Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense, Avda. Jose Antonio Nováis 12, 28040, Madrid, Spain
| | - Alexandre Salino
- Programa de Pós-Graduação em Biologia Vegetal, Universidade Federal de Minas Gerais, P.O. Box 486, 31270-901, Belo Horizonte, MG, Brazil
| | | | - Emily B Sessa
- Department of Biology, 876 Newell Drive, University of Florida, Gainesville, FL, 32611, USA
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Kuo L, Tang SK, Kao T, Ebihara A, Fawcett S, Hsiao M, Shinohara W, Dauphin B. A dormant resource for genome size estimation in ferns: C-value inference of the Ophioglossaceae using herbarium specimen spores. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11452. [PMID: 34938613 PMCID: PMC8664048 DOI: 10.1002/aps3.11452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
PREMISE The great variation of genome size (C-value) across land plants is linked to various adaptative features. Flow cytometry (FCM), the standard approach to estimating C-values, relies mostly on fresh materials, performing poorly when used with herbarium materials. No fern C-value reports have been derived from herbarium specimens; however, the herbarium spores of some ferns remain highly viable for decades and are thus promising for further investigation. To explore this possibility, we evaluated herbarium spore collections of Ophioglossaceae ferns using FCM. METHODS Flow cytometry was conducted on 24 spore samples, representing eight of the 12 genera of the Ophioglossaceae, using specimens ranging in age from 2.6 to 111 years obtained from five herbaria. RESULTS Regardless of the genus or the source herbarium, high-quality C-value data were generated from 17 samples, with the oldest being 26 years old. Estimates of the C-values from sporophytic tissues of known ploidy did not reveal any evidence of apomixis for the species surveyed here. We also detected a pronounced genome downsizing in Sceptridium polyploids. DISCUSSION The recent success of FCM for C-value estimation using spores provides a much more convenient method of utilizing "dry" refrigerated materials. We demonstrate here that herbarium spores of some ferns are also promising for this use, even for older specimens.
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Affiliation(s)
- Li‐Yaung Kuo
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Sheng Kai Tang
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Tzu‐Tong Kao
- Department of BiologyDuke UniversityDurhamNorth CarolinaUSA
- Institute of Plant and Microbial BiologyAcademia SinicaTaipei CityTaiwan
| | - Atsushi Ebihara
- Department of BotanyNational Museum of Nature and Science, TsukubaIbarakiJapan
| | - Susan Fawcett
- University and Jepson Herbaria, University of California, BerkeleyCaliforniaUSA
| | - Min‐Chien Hsiao
- Institute of Ecology and Evolutionary BiologyNational Taiwan UniversityTaipei CityTaiwan
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Meudt HM, Albach DC, Tanentzap AJ, Igea J, Newmarch SC, Brandt AJ, Lee WG, Tate JA. Polyploidy on Islands: Its Emergence and Importance for Diversification. FRONTIERS IN PLANT SCIENCE 2021; 12:637214. [PMID: 33763097 PMCID: PMC7982887 DOI: 10.3389/fpls.2021.637214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/11/2021] [Indexed: 05/31/2023]
Abstract
Whole genome duplication or polyploidy is widespread among floras globally, but traditionally has been thought to have played a minor role in the evolution of island biodiversity, based on the low proportion of polyploid taxa present. We investigate five island systems (Juan Fernández, Galápagos, Canary Islands, Hawaiian Islands, and New Zealand) to test whether polyploidy (i) enhances or hinders diversification on islands and (ii) is an intrinsic feature of a lineage or an attribute that emerges in island environments. These island systems are diverse in their origins, geographic and latitudinal distributions, levels of plant species endemism (37% in the Galapagos to 88% in the Hawaiian Islands), and ploidy levels, and taken together are representative of islands more generally. We compiled data for vascular plants and summarized information for each genus on each island system, including the total number of species (native and endemic), generic endemicity, chromosome numbers, genome size, and ploidy levels. Dated phylogenies were used to infer lineage age, number of colonization events, and change in ploidy level relative to the non-island sister lineage. Using phylogenetic path analysis, we then tested how the diversification of endemic lineages varied with the direct and indirect effects of polyploidy (presence of polyploidy, time on island, polyploidization near colonization, colonizer pool size) and other lineage traits not associated with polyploidy (time on island, colonizer pool size, repeat colonization). Diploid and tetraploid were the most common ploidy levels across all islands, with the highest ploidy levels (>8x) recorded for the Canary Islands (12x) and New Zealand (20x). Overall, we found that endemic diversification of our focal island floras was shaped by polyploidy in many cases and certainly others still to be detected considering the lack of data in many lineages. Polyploid speciation on the islands was enhanced by a larger source of potential congeneric colonists and a change in ploidy level compared to overseas sister taxa.
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Affiliation(s)
- Heidi M Meudt
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Dirk C Albach
- Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Andrew J Tanentzap
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Javier Igea
- Ecosystems and Global Change Group, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Sophie C Newmarch
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | | | - William G Lee
- Manaaki Whenua - Landcare Research, Dunedin, New Zealand
| | - Jennifer A Tate
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Murdock AG, Chen CW, Huang YM, Glenny D. Affinities of the fern genus Ptisana (Marattiaceae) in the Solomon Islands, with descriptions of two new species. PHYTOKEYS 2020; 170:1-23. [PMID: 33363432 PMCID: PMC7746669 DOI: 10.3897/phytokeys.170.59471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/20/2020] [Indexed: 06/12/2023]
Abstract
In the process of undertaking a comprehensive review of the pteridophytes of the Solomon Islands, multiple unidentified specimens of the fern genus Ptisana Murdock (Marattiaceae) were collected. Morphological and molecular phylogenetic analyses as well as field observations were required to identify the Solomon Islands taxa. Four species and one variety are recognized from the Solomon Islands: Ptisana ambulans Murdock & C.W. Chen, sp. nov., Ptisana decipiens Murdock & C.W. Chen, sp. nov., Ptisana decipiens var. delicata Murdock & C.W. Chen, var. nov., Ptisana papuana (Alderw.) Murdock & C.W. Chen, comb. nov., and Ptisana smithii (Mett. ex Kuhn) Murdock. The complexities in the identification of Solomon Islands collections show the limits of morphology in the genus and illuminate a path forward for untangling the Ptisana taxonomy on a broader scale.
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Affiliation(s)
- Andrew G. Murdock
- Innovative Genomics Institute, University of California, Berkeley, 2151 Berkeley Way, Berkeley, California 94720, USA
- University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building, Berkeley, California 94720, USA
| | - Cheng-Wei Chen
- No. 37, Lane 656, Chung Cheng Rd., Keelung City, 20246, Taiwan
| | - Yao-Moan Huang
- Taiwan Forestry Research Institute, No. 53, Nanhai Rd, Zhongzheng District, Taipei City, 10066, Taiwan
| | - David Glenny
- Allan Herbarium, Manaaki Whenua, PO Box 40, Lincoln 7640, New Zealand
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Hori K. Deparia × nanakuraensis K.Hori (Athyriaceae), a new hybrid pteridophyte from Japan. PHYTOKEYS 2020; 165:69-84. [PMID: 33192147 PMCID: PMC7642121 DOI: 10.3897/phytokeys.165.57837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
I describe Deparia × nanakuraensishyb. nov. and discuss differences in morphological characteristics between parental species D. pterorachis and D. viridifrons with chromosome counting, plastid, and nuclear DNA markers. The new hybrid is endemic to the eastern and northern parts of Japan. Based on the criteria of the International Union for Conservation of Nature and Natural Resources, this new species is here considered Data Deficient. The ploidy level is diploid sterile.
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Affiliation(s)
- Kiyotaka Hori
- The Kochi prefectural Makino Botanical Garden, Kochi, JapanThe Kochi prefectural Makino Botanical GardenKochiJapan
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7
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Kuo LY, Chang YH, Huang YH, Testo W, Ebihara A, Rouhan G, Quintanilla LG, Watkins JE, Huang YM, Li FW. A global phylogeny of Stegnogramma ferns (Thelypteridaceae): generic and sectional revision, historical biogeography and evolution of leaf architecture. Cladistics 2020; 36:164-183. [PMID: 34618958 DOI: 10.1111/cla.12399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2019] [Indexed: 10/26/2022] Open
Abstract
The thelypteroid fern genus Stegnogramma s.l. contains around 18-35 species and has a global, cross-continental distribution ranging from tropical to temperate regions. Several genera and infrageneric sections have been recognized previously in Stegnogramma s.l., but their phylogenetic relationships are still unclear. In this study, we present a global phylogeny of Stegnogramma s.l. with the most comprehensive sampling to date and aim to pinpoint the phylogenetic positions of biogeographically and taxonomically important taxa. Based on the reconstructed historical biogeography and character evolution, we propose a new (infra)generic classification and discuss the diversification of Stegnogramma s.l. in a biogeographical context. New names or combinations are made for 12 (infra)species, including transferring the monotypic species of Craspedosorus to Leptogramma. Finally, we discuss a possible link between leaf architecture and ecological adaptation, and hypothesize that the increase in leaf dissection and free-vein proportion is an adaptive feature to cool climates in Stegnogramma s.l.
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Affiliation(s)
- Li-Yaung Kuo
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.,Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Yi-Hang Chang
- Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
| | - Yu-Hsuan Huang
- Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
| | - Weston Testo
- Biology Department, University of Florida, Gainesville, FL, 32611, USA
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki, 305-0005, Japan
| | - Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, EPHE, Sorbonne Université, 16 rue Buffon CP39, F-75005, Paris, France
| | - Luis G Quintanilla
- School of Environmental Sciences and Technology, Rey Juan Carlos University, Móstoles, Spain
| | - James E Watkins
- Department of Biology, Colgate University, Hamilton, NY, 13346, USA
| | - Yao-Moan Huang
- Taiwan Forestry Research Institute, Taipei, 10066, Taiwan
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA.,Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
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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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Ebihara A, Nitta JH. An update and reassessment of fern and lycophyte diversity data in the Japanese Archipelago. JOURNAL OF PLANT RESEARCH 2019. [PMID: 31529289 DOI: 10.5061/dryad.4362p32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The fern and lycophyte flora of Japan comprising 721 native taxa (including subspecies and varieties) plus 371 interspecific hybrids was reassessed using a nearly comprehensively sampled distribution map at 10 km resolution vouchered by 216,687 specimens, up-to-date cytotaxonomic information covering 74% of the taxa, and an rbcL sequence dataset covering 97.9% of the taxa. Spatial distribution of species richness and phylogenetic diversity was visualized. Apomixis was observed in 11.0% of the native taxa whose reproductive modes are known. The number of sexually reproducing polyploid taxa (n = 199) is less than sexual diploids (n = 241), and 30 of them are evidently allopolyploid, in contrast with the low number of possible autopolyploids (n = 4). Apomictic taxa were found to have smaller latitudinal ranges than sexual taxa or taxa with multiple reproductive modes. A morphological character dataset in Lucid format is provided for taxonomic identification of the native taxa.
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Affiliation(s)
- Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan.
| | - Joel H Nitta
- Department of Botany, National Museum of Natural History, Smithsonian Institute, Washington, DC, 20013, USA
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Ebihara A, Nitta JH. An update and reassessment of fern and lycophyte diversity data in the Japanese Archipelago. JOURNAL OF PLANT RESEARCH 2019; 132:723-738. [PMID: 31529289 PMCID: PMC6831535 DOI: 10.1007/s10265-019-01137-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/31/2019] [Indexed: 05/14/2023]
Abstract
The fern and lycophyte flora of Japan comprising 721 native taxa (including subspecies and varieties) plus 371 interspecific hybrids was reassessed using a nearly comprehensively sampled distribution map at 10 km resolution vouchered by 216,687 specimens, up-to-date cytotaxonomic information covering 74% of the taxa, and an rbcL sequence dataset covering 97.9% of the taxa. Spatial distribution of species richness and phylogenetic diversity was visualized. Apomixis was observed in 11.0% of the native taxa whose reproductive modes are known. The number of sexually reproducing polyploid taxa (n = 199) is less than sexual diploids (n = 241), and 30 of them are evidently allopolyploid, in contrast with the low number of possible autopolyploids (n = 4). Apomictic taxa were found to have smaller latitudinal ranges than sexual taxa or taxa with multiple reproductive modes. A morphological character dataset in Lucid format is provided for taxonomic identification of the native taxa.
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Affiliation(s)
- Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki, 305-0005, Japan.
| | - Joel H Nitta
- Department of Botany, National Museum of Natural History, Smithsonian Institute, Washington, DC, 20013, USA
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Viruel J, Conejero M, Hidalgo O, Pokorny L, Powell RF, Forest F, Kantar MB, Soto Gomez M, Graham SW, Gravendeel B, Wilkin P, Leitch IJ. A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens. FRONTIERS IN PLANT SCIENCE 2019; 10:937. [PMID: 31396248 PMCID: PMC6667659 DOI: 10.3389/fpls.2019.00937] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 07/04/2019] [Indexed: 05/24/2023]
Abstract
Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam (Dioscorea) tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy (Dioscorea alata, D. communis, and D. sylvatica). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of Dioscorea. We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.
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Affiliation(s)
- Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Laboratori de Botànica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawai’i at Mânoa, Honolulu, HI, United States
| | - Marybel Soto Gomez
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, BC, Canada
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Endless Forms, Leiden, Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
- Science and Technology Faculty, University of Applied Sciences Leiden, Leiden, Netherlands
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
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Shaw AJ, Carter BE, Aguero B, da Costa DP, Crowl AA. Range change evolution of peat mosses (Sphagnum) within and between climate zones. GLOBAL CHANGE BIOLOGY 2019; 25:108-120. [PMID: 30346105 DOI: 10.1111/gcb.14485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Peat mosses (Sphagnum) hold exceptional importance in the control of global carbon fluxes and climate because of the vast stores of carbon bound up in partially decomposed biomass (peat). This study tests the hypothesis that the early diversification of Sphagnum was in the Northern Hemisphere, with subsequent range expansions to tropical latitudes and the Southern Hemisphere. A phylogenetic analysis of 192 accessions representing the moss class Sphagnopsida based on four plastid loci was conducted in conjunction with biogeographic analyses using BioGeoBEARS to investigate the tempo and mode of geographic range evolution. Analyses support the hypothesis that the major intrageneric clades of peat-forming species accounting for >90% of peat moss diversity originated and diversified at northern latitudes. The genus underwent multiple range expansions into tropical and Southern Hemisphere regions. Range evolution in peat mosses was most common within latitudinal zones, attesting to the relative difficulty of successfully invading new climate zones. Allopolyploidy in Sphagnum (inferred from microsatellite heterozygosity) does not appear to be biased with regard to geographic region nor intrageneric clade. The inference that Sphagnum diversified in cool-or cold-climate regions and repeatedly expanded its range into tropical regions makes the genus an excellent model for studying morphological, physiological, and genomic traits associated with adaptation to warming climates.
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Affiliation(s)
- A Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina
| | - Benjamin E Carter
- Department of Biological Sciences, San Jose State University, San Jose, California
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, North Carolina
| | | | - Andrew A Crowl
- Department of Biology, Duke University, Durham, North Carolina
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13
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Wallis GP, Jorge F. Going under down under? Lineage ages argue for extensive survival of the Oligocene marine transgression on Zealandia. Mol Ecol 2018; 27:4368-4396. [DOI: 10.1111/mec.14875] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/08/2018] [Accepted: 09/10/2018] [Indexed: 01/05/2023]
Affiliation(s)
| | - Fátima Jorge
- Department of Zoology; University of Otago; Dunedin New Zealand
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14
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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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15
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Song M, Kuo LY, Huiet L, Pryer KM, Rothfels CJ, Li FW. A novel chloroplast gene reported for flagellate plants. AMERICAN JOURNAL OF BOTANY 2018. [PMID: 29532931 DOI: 10.1002/ajb2.1010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
PREMISE OF THE STUDY Gene space in plant plastid genomes is well characterized and annotated, yet we discovered an unrecognized open reading frame (ORF) in the fern lineage that is conserved across flagellate plants. METHODS We initially detected a putative uncharacterized ORF by the existence of a highly conserved region between rps16 and matK in a series of matK alignments of leptosporangiate ferns. We mined available plastid genomes for this ORF, which we now refer to as ycf94, to infer evolutionary selection pressures and assist in functional prediction. To further examine the transcription of ycf94, we assembled the plastid genome and sequenced the transcriptome of the leptosporangiate fern Adiantum shastense Huiet & A.R. Sm. KEY RESULTS The ycf94 predicted protein has a distinct transmembrane domain but with no sequence homology to other proteins with known function. The nonsynonymous/synonymous substitution rate ratio of ycf94 is on par with other fern plastid protein-encoding genes, and additional homologs can be found in a few lycophyte, moss, hornwort, and liverwort plastid genomes. Homologs of ycf94 were not found in seed plants. In addition, we report a high level of RNA editing for ycf94 transcripts-a hallmark of protein-coding genes in fern plastomes. CONCLUSIONS The degree of sequence conservation, together with the presence of a distinct transmembrane domain and RNA-editing sites, suggests that ycf94 is a protein-coding gene of functional significance in ferns and, potentially, bryophytes and lycophytes. However, the origin and exact function of this gene require further investigation.
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Affiliation(s)
- Michael Song
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
| | - Li-Yaung Kuo
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Section of Plant Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina, 27708, USA
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, California, 94720, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Section of Plant Biology, Cornell University, Ithaca, New York, 14853, USA
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16
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Wei X, Qi Y, Zhang X, Luo L, Shang H, Wei R, Liu H, Zhang B. Phylogeny, historical biogeography and characters evolution of the drought resistant fern Pyrrosia Mirbel (Polypodiaceae) inferred from plastid and nuclear markers. Sci Rep 2017; 7:12757. [PMID: 28986552 PMCID: PMC5630607 DOI: 10.1038/s41598-017-12839-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/14/2017] [Indexed: 11/09/2022] Open
Abstract
Pyrrosia s.l. comprises ca. 60 species with a disjunct Africa/Asia and Australia distribution. The infrageneric classification of Pyrrosia s.l. is controversial based on the phylogenetic analyses of chloroplast markers and morphology. Based on the expanded taxon sampling of Pyrrosia s.l. (51 species), we investigated its phylogeny, biogeography, character evolution and environmental adaptation by employing five chloroplastid markers (rbcL, matK, psbA-trnH, and rps4 + rps4-trnS) and one single (low)-copy nuclear gene, LEAFY. Pyrrosia s.l. was divided into six major clades and eight subclades. Reticulate evolution was revealed both among clades and among species in Pyrrosia s.l. Ancestral character state optimization revealed high levels of homoplastic evolution of the diagnostic characters in Pyrrosia s.l., while the crassulacean acid metabolism pathway seems to have an independent origin. Molecular dating and biogeographic diversification analyses suggested that Pyrrosia s.l. originated no later than the Oligocene and the main clades diversified during the Oligocene and Miocene, with southern Asia, the Indo-China Peninsula and southwestern and southern China as the most likely ancestral areas. Transoceanic long-distance dispersal, rather than vicariance, contributed to the intercontinental disjunction. Diversification scenarios of Pyrrosia s.l. under geological movements and climate fluctuation are also discussed.
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Affiliation(s)
- Xueping Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yaodong Qi
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Luo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hui Shang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences; Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Haitao Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Bengang Zhang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
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17
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Hennequin S, Rouhan G, Salino A, Duan YF, Lepeigneux MC, Guillou M, Ansell S, Almeida TE, Zhang LB, Schneider H. Global phylogeny and biogeography of the fern genus Ctenitis (Dryopteridaceae), with a focus on the Indian Ocean region. Mol Phylogenet Evol 2017; 112:277-289. [DOI: 10.1016/j.ympev.2017.04.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/10/2017] [Indexed: 12/24/2022]
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18
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Madagascar sheds new light on the molecular systematics and biogeography of grammitid ferns: New unexpected lineages and numerous long-distance dispersal events. Mol Phylogenet Evol 2017; 111:1-17. [DOI: 10.1016/j.ympev.2017.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 12/22/2022]
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19
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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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