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Lundquist CR, Rudall PJ, Sukri RS, Conejero M, Smith A, Lopez-Garcia M, Vignolini S, Metali F, Whitney HM. Living jewels: iterative evolution of iridescent blue leaves from helicoidal cell walls. ANNALS OF BOTANY 2024; 134:131-150. [PMID: 38551515 PMCID: PMC11161568 DOI: 10.1093/aob/mcae045] [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: 02/08/2024] [Accepted: 04/15/2024] [Indexed: 06/09/2024]
Abstract
BACKGROUND AND AIMS Structural colour is responsible for the remarkable metallic blue colour seen in the leaves of several plants. Species belonging to only ten genera have been investigated to date, revealing four photonic structures responsible for structurally coloured leaves. One of these is the helicoidal cell wall, known to create structural colour in the leaf cells of five taxa. Here we investigate a broad selection of land plants to understand the phylogenetic distribution of this photonic structure in leaves. METHODS We identified helicoidal structures in the leaf epidermal cells of 19 species using transmission electron microscopy. Pitch measurements of the helicoids were compared with the reflectance spectra of circularly polarized light from the cells to confirm the structure-colour relationship. RESULTS By incorporating species examined with a polarizing filter, our results increase the number of taxa with photonic helicoidal cell walls to species belonging to at least 35 genera. These include 19 monocot genera, from the orders Asparagales (Orchidaceae) and Poales (Cyperaceae, Eriocaulaceae, Rapateaceae) and 16 fern genera, from the orders Marattiales (Marattiaceae), Schizaeales (Anemiaceae) and Polypodiales (Blechnaceae, Dryopteridaceae, Lomariopsidaceae, Polypodiaceae, Pteridaceae, Tectariaceae). CONCLUSIONS Our investigation adds considerably to the recorded diversity of plants with structurally coloured leaves. The iterative evolution of photonic helicoidal walls has resulted in a broad phylogenetic distribution, centred on ferns and monocots. We speculate that the primary function of the helicoidal wall is to provide strength and support, so structural colour could have evolved as a potentially beneficial chance function of this structure.
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Affiliation(s)
- Clive R Lundquist
- School of Biological Sciences, University of Bristol, Bristol, UK
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Paula J Rudall
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Rahayu S Sukri
- Faculty of Science, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei Darussalam
| | - María Conejero
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK
| | - Alyssa Smith
- Department of Chemistry, University of Cambridge, UK
| | - Martin Lopez-Garcia
- Department of Nanophotonics, International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - Silvia Vignolini
- Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Faizah Metali
- Faculty of Science, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei Darussalam
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Chamberland L, Agnarsson I, Quayle IL, Ruddy T, Starrett J, Bond JE. Biogeography and eye size evolution of the ogre-faced spiders. Sci Rep 2022; 12:17769. [PMID: 36273015 PMCID: PMC9588044 DOI: 10.1038/s41598-022-22157-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 10/10/2022] [Indexed: 01/19/2023] Open
Abstract
Net-casting spiders (Deinopidae) comprise a charismatic family with an enigmatic evolutionary history. There are 67 described species of deinopids, placed among three genera, Deinopis, Menneus, and Asianopis, that are distributed globally throughout the tropics and subtropics. Deinopis and Asianopis, the ogre-faced spiders, are best known for their giant light-capturing posterior median eyes (PME), whereas Menneus does not have enlarged PMEs. Molecular phylogenetic studies have revealed discordance between morphology and molecular data. We employed a character-rich ultra-conserved element (UCE) dataset and a taxon-rich cytochrome-oxidase I (COI) dataset to reconstruct a genus-level phylogeny of Deinopidae, aiming to investigate the group's historical biogeography, and examine PME size evolution. Although the phylogenetic results support the monophyly of Menneus and the single reduction of PME size in deinopids, these data also show that Deinopis is not monophyletic. Consequently, we formally transfer 24 Deinopis species to Asianopis; the transfers comprise all of the African, Australian, South Pacific, and a subset of Central American and Mexican species. Following the divergence of Eastern and Western deinopids in the Cretaceous, Deinopis/Asianopis dispersed from Africa, through Asia and into Australia with its biogeographic history reflecting separation of Western Gondwana as well as long-distance dispersal events.
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Affiliation(s)
- Lisa Chamberland
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Ingi Agnarsson
- grid.14013.370000 0004 0640 0021Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 102 Reykjavik, Iceland
| | - Iris L. Quayle
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Tess Ruddy
- grid.267778.b0000 0001 2290 5183Vassar College, Poughkeepsie, NY 12604 USA
| | - James Starrett
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
| | - Jason E. Bond
- grid.27860.3b0000 0004 1936 9684Department of Entomology and Nematology, University of California Davis, Davis, CA 95616 USA
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Vasco A, Matos FB, Sundue MA. Robbin C. Moran, Fern and Lycophyte Curator- an Appreciation. THE BOTANICAL REVIEW; INTERPRETING BOTANICAL PROGRESS 2021; 87:151-166. [PMID: 34219751 PMCID: PMC8241203 DOI: 10.1007/s12229-021-09254-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
To mark the commencement of his retirement as Nathaniel Lord Britton Curator of Botany, and appointment as Curator Emeritus at the New York Botanical Garden, we pay tribute to Robbin Moran and impact on the botanical community with a brief synopsis of his career. Naturalist, fern expert, adored teacher-it is difficult to adequately pay tribute to his accomplishments, and his impact on botany in a single article. Robbin has published four books, 13 monographs of neotropical fern clades, over 170 scientific papers, and dozens of popular articles. He has named 115 new species, five new genera, and one family of ferns. He is eponymized by seven new species and the genus Moranopteris. We recount his earliest days and academic trajectory to become a leading researcher and educator in pteridology. We highlight his major influences, scientific accomplishments, and outreach to the botanical community.
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Affiliation(s)
- Alejandra Vasco
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX 76107 USA
| | - Fernando B. Matos
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Av. Purdue s.n., Viçosa, Minas Gerais CEP 36570-900 Brazil
| | - Michael A. Sundue
- Department of Plant Biology, The Pringle Herbarium, University of Vermont, 111 Jeffords Hall, Burlington, 05405 VT USA
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Rouhan G. Synoptic revision of the fern genus Elaphoglossum Schott ex J.Sm. (Dryopteridaceae) in Madagascar, with the description of 23 new taxa, all but one endemic. PeerJ 2021; 8:e10484. [PMID: 33391872 PMCID: PMC7759133 DOI: 10.7717/peerj.10484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/12/2020] [Indexed: 11/20/2022] Open
Abstract
After 15 years of field studies in Madagascar, especially focused on the overlooked fern genus Elaphoglossum (Dryopteridaceae), a synoptic revision of the genus is here presented. Based on more than 2,600 herbarium specimens including collections over 200 years, Elaphoglossum is the second most diversified fern genus in Madagascar, with 52 species and three subspecies (with 76% of endemism). It is to be compared to the 34 species treated by Tardieu-Blot in 1960 for the "Flore de Madagascar et des Comores" or the 38 species listed by Roux in 2009 in the seminal "Synopsis of the Lycopodiophyta and Pteridophyta of Africa, Madagascar and neighboring islands". The 55 taxa represent five out of seven existing generic sections (sect. Amygdalifolia and sect. Wrightiana being monotypic and Neotropical): sect. Lepidoglossa (29 spp. and three subspp.), sect. Elaphoglossum (17 spp.), sect. Setosa (3 spp.), sect. Squamipedia (2 spp.), and sect. Polytrichia (1 sp.). Distribution is given for each species and subspecies, and detailed for each island or archipelago in the Western Indian Ocean (La Réunion, Mauritius, Seychelles, and Comoros). Twenty species and three subspecies are newly described, all but one endemic to Madagascar: Elaphoglossum ambrense Rouhan, Elaphoglossum andohahelense Rouhan, Elaphoglossum anjanaharibense Rouhan, Elaphoglossum approximatum Rouhan, Elaphoglossum brachymischum Rouhan, Elaphoglossum cerussatum Tardieu subsp. brunneum Rouhan, Elaphoglossum coracinolepis Rouhan, Elaphoglossum desireanum Rouhan, Elaphoglossum glabricaule Rouhan, Elaphoglossum gladiifolium Rouhan, Elaphoglossum leucolepis (Baker) Krajina ex Tardieu subsp. nanolepis Rouhan, Elaphoglossum leucolepis (Baker) Krajina ex Tardieu subsp. nigricans Rouhan, Elaphoglossum longiacuminatum Rouhan, Elaphoglossum patriceanum Rouhan, Elaphoglossum perangustum Rouhan, Elaphoglossum prominentinervulum Rouhan, Elaphoglossum rakotondrainibeae Rouhan, Elaphoglossum repandum Rouhan, Elaphoglossum sabineanum Rouhan, Elaphoglossum sinensiumbrarum Rouhan, Elaphoglossum subglabricaule Rouhan, Elaphoglossum tsaratananense Rouhan, and Elaphoglossum viridicaule Rouhan. Morphological description, distribution map, and original illustrations are provided for each new taxon. Novel identification keys to the sections and all species from Madagascar are also presented.
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Affiliation(s)
- Germinal Rouhan
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS; Paris, France
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Bauret L, Field AR, Gaudeul M, Selosse MA, Rouhan G. First insights on the biogeographical history of Phlegmariurus (Lycopodiaceae), with a focus on Madagascar. Mol Phylogenet Evol 2018; 127:488-501. [DOI: 10.1016/j.ympev.2018.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 05/01/2018] [Accepted: 05/03/2018] [Indexed: 10/17/2022]
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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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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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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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Sundue MA, Testo WL, Ranker TA. Morphological innovation, ecological opportunity, and the radiation of a major vascular epiphyte lineage. Evolution 2015; 69:2482-95. [DOI: 10.1111/evo.12749] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 07/19/2015] [Accepted: 07/23/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Michael A. Sundue
- Department of Plant Biology; University of Vermont, Pringle Herbarium; 27 Colchester Avenue Burlington Vermont 05405
| | - Weston L. Testo
- Department of Plant Biology; University of Vermont, Pringle Herbarium; 27 Colchester Avenue Burlington Vermont 05405
| | - Tom A. Ranker
- Department of Botany; University of Hawai'i at Mānoa; 3190 Maile Way Honolulu Hawaii 96822
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Chao YS, Rouhan G, Amoroso VB, Chiou WL. Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae). ANNALS OF BOTANY 2014; 114:109-24. [PMID: 24908681 PMCID: PMC4071104 DOI: 10.1093/aob/mcu086] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/31/2014] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS Pteris (Pteridaceae), comprising over 250 species, had been thought to be a monophyletic genus until the three monotypic genera Neurocallis, Ochropteris and Platyzoma were included. However, the relationships between the type species of the genus Pteris, P. longifolia, and other species are still unknown. Furthermore, several infrageneric morphological classifications have been proposed, but are debated. To date, no worldwide phylogenetic hypothesis has been proposed for the genus, and no comprehensive biogeographical history of Pteris, crucial to understanding its cosmopolitan distribution, has been presented. METHODS A molecular phylogeny of Pteris is presented for 135 species, based on cpDNA rbcL and matK and using maximum parsimony, maximum likelihood and Bayesian inference approaches. The inferred phylogeny was used to assess the biogeographical history of Pteris and to reconstruct the evolution of one ecological and four morphological characters commonly used for infrageneric classifications. KEY RESULTS The monophyly of Pteris remains uncertain, especially regarding the relationship of Pteris with Actiniopteris + Onychium and Platyzoma. Pteris comprises 11 clades supported by combinations of ecological and morphological character states, but none of the characters used in previous classifications were found to be exclusive synapomorphies. The results indicate that Pteris diversified around 47 million years ago, and when species colonized new geographical areas they generated new lineages, which are associated with morphological character transitions. CONCLUSIONS This first phylogeny of Pteris on a global scale and including more than half of the diversity of the genus should contribute to a new, more reliable infrageneric classification of Pteris, based not only on a few morphological characters but also on ecological traits and geographical distribution. The inferred biogeographical history highlights long-distance dispersal as a major process shaping the worldwide distribution of the species. Colonization of different niches was followed by subsequent morphological diversification. Dispersal events followed by allopatric and parapatric speciation contribute to the species diversity of Pteris.
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Affiliation(s)
- Yi-Shan Chao
- The Experimental Forest, National Taiwan University, Nantou, Taiwan Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Germinal Rouhan
- Muséum national d'Histoire naturelle, UMR CNRS 7205, Herbier National, 16 rue Buffon CP39, 75005 Paris, France
| | | | - Wen-Liang Chiou
- Division of Botanical Garden, Taiwan Forestry Research Institute, Taipei, Taiwan
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Korall P, Pryer KM. Global biogeography of scaly tree ferns (Cyatheaceae): evidence for Gondwanan vicariance and limited transoceanic dispersal. JOURNAL OF BIOGEOGRAPHY 2014; 41:402-413. [PMID: 25435648 PMCID: PMC4238398 DOI: 10.1111/jbi.12222] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
AIM Scaly tree ferns, Cyatheaceae, are a well-supported group of mostly tree-forming ferns found throughout the tropics, the subtropics and the south-temperate zone. Fossil evidence shows that the lineage originated in the Late Jurassic period. We reconstructed large-scale historical biogeographical patterns of Cyatheaceae and tested the hypothesis that some of the observed distribution patterns are in fact compatible, in time and space, with a vicariance scenario related to the break-up of Gondwana. LOCATION Tropics, subtropics and south-temperate areas of the world. METHODS The historical biogeography of Cyatheaceae was analysed in a maximum likelihood framework using Lagrange. The 78 ingroup taxa are representative of the geographical distribution of the entire family. The phylogenies that served as a basis for the analyses were obtained by Bayesian inference analyses of mainly previously published DNA sequence data using MrBayes. Lineage divergence dates were estimated in a Bayesian Markov chain Monte Carlo framework using beast. RESULTS Cyatheaceae originated in the Late Jurassic in either South America or Australasia. Following a range expansion, the ancestral distribution of the marginate-scaled clade included both these areas, whereas Sphaeropteris is reconstructed as having its origin only in Australasia. Within the marginate-scaled clade, reconstructions of early divergences are hampered by the unresolved relationships among the Alsophila, Cyathea and Gymnosphaera lineages. Nevertheless, it is clear that the occurrence of the Cyathea and Sphaeropteris lineages in South America may be related to vicariance, whereas transoceanic dispersal needs to be inferred for the range shifts seen in Alsophila and Gymnosphaera. MAIN CONCLUSIONS The evolutionary history of Cyatheaceae involves both Gondwanan vicariance scenarios as well as long-distance dispersal events. The number of transoceanic dispersals reconstructed for the family is rather few when compared with other fern lineages. We suggest that a causal relationship between reproductive mode (outcrossing) and dispersal limitations is the most plausible explanation for the pattern observed.
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Affiliation(s)
- Petra Korall
- Systematic Biology, Evolutionary Biology Centre, Uppsala UniversityNorbyvägen 18D, SE-752 36, Uppsala, Sweden
- *Correspondence: P. Korall, Systematic Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden. E-mail:
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Macedo TS, Góes Neto A, Nonato FR. Análise florística e fitogeografia das samambaias e licófitas de um fragmento de Mata Atlântica na Serra da Jibóia, Santa Teresinha, Bahia, Brasil. RODRIGUÉSIA 2013. [DOI: 10.1590/s2175-78602013000300008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
O trabalho apresenta espécies de samambaias e licófitas de um fragmento de Mata Atlântica, inserido na região de semi-árido, localizado na Serra da Jibóia, Município de Santa Teresinha, Bahia, Brasil e a análise das relações florísticas com outras formações vegetais do país, contribuindo para ampliar as informações sobre a flora vascular do estado, bem como do bioma Mata Atlântica. São apresentadas 97 espécies, em 51 gêneros e 22 famílias. As famílias mais representativas foram Dryopteridaceae (17 spp.), Polypodiaceae (16 spp.), Pteridaceae (12 spp.) e Hymenophyllaceae (10 spp.). A maioria das espécies ocorre como epífita (48%), 38% terrestre, 3% rupícola, 3% como hemiepífita e 8% com mais de um tipo de hábito. A análise de similaridade mostra que a flora de samambaias e licófitas da região está relacionada com o Sul da Bahia e Sudeste do Brasil, sugerindo que a área de estudo apresenta condições ambientais semelhantes às áreas relacionadas e reforçando as singularidades florísticas da região.
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Sessa EB, Zimmer EA, Givnish TJ. Unraveling reticulate evolution in North American Dryopteris (Dryopteridaceae). BMC Evol Biol 2012; 12:104. [PMID: 22748145 PMCID: PMC3509404 DOI: 10.1186/1471-2148-12-104] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 06/14/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The thirteen species of Dryopteris in North America have long been suspected of having undergone a complicated history of reticulate evolution via allopolyploid hybridization. Various explanations for the origins of the allopolyploid taxa have been suggested, and though most lines of evidence have supported the so-called "semicristata" hypothesis, contention over the group's history has continued in several recent, conflicting studies. RESULTS Sequence data from nine plastid and two nuclear markers were collected from 73 accessions representing 35 species of Dryopteris. Sequences from each of the allopolyploids are most closely related to their progenitor species as predicted by the "semicristata" hypothesis. Allotetraploid D. campyloptera appears to be derived from a hybrid between diploid D. expansa and D. intermedia; D. celsa, from diploid D. ludoviciana x D. goldiana; and D. carthusiana and D. cristata, from diploid "D. semicristata" x D. intermedia and D. ludoviciana, respectively. Allohexaploid D. clintoniana appears to be derived from D. cristata x D.goldiana. The earliest estimated dates of formation of the allopolyploids, based on divergence time analyses, were within the last 6 Ma. We found no evidence for recurrent formation of any of the allopolyploids. The sexual allopolyploid taxa are derived from crosses between parents that show intermediate levels of genetic divergence relative to all pairs of potential progenitors. In addition, the four allotetraploids are transgressive with respect to geographic range relative to one or both of their parents (their ranges extend beyond those of the parents), suggesting that ecological advantages in novel habitats or regions may promote long-term regional coexistence of the hybrid taxa with their progenitors. CONCLUSIONS This study provides the first thorough evaluation of the North American complex of woodferns using extensive sampling of taxa and genetic markers. Phylogenies produced from each of three datasets (one plastid and two nuclear) support the "semicristata" hypothesis, including the existence of a missing diploid progenitor, and allow us to reject all competing hypotheses. This study demonstrates the value of using multiple, biparentally inherited markers to evaluate reticulate complexes, assess the frequency of recurrent polyploidization, and determine the relative importance of introgression vs. hybridization in shaping the histories of such groups.
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Affiliation(s)
- Emily B Sessa
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013-7012, USA
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
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Sessa EB, Zimmer EA, Givnish TJ. Phylogeny, divergence times, and historical biogeography of New World Dryopteris (Dryopteridaceae). AMERICAN JOURNAL OF BOTANY 2012; 99:730-750. [PMID: 22434775 DOI: 10.3732/ajb.1100294] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Dryopteris is a large, cosmopolitan fern genus ideal for addressing questions about diversification, biogeography, hybridization, and polyploidy, which have historically been understudied in ferns. We constructed a highly resolved, well-supported phylogeny for New World Dryopteris and used it to investigate biogeographic patterns and divergence times. METHODS We analyzed relationships among 97 species of Dryopteris, including taxa from all major biogeographic regions, with analyses based on 5699 aligned nucleotides from seven plastid loci. Phylogenetic analyses used maximum parsimony, maximum likelihood, and Bayesian inference. We conducted divergence time analyses using BEAST and biogeographic analyses using maximum parsimony, maximum likelihood, Bayesian, and S-DIVA approaches. We explored the monophyly of subgenera and sections in the most recent generic classification and of geographic groups of taxa using Templeton tests. KEY RESULTS The genus Dryopteris arose ca. 42 million years ago (Ma). Most of the Central and South American species form a well-supported clade which arose 32 Ma, but the remaining New World species are the result of multiple, independent dispersal and vicariance events involving Asia, Europe, and Africa over the last 15 Myr. We identified six long-distance dispersal events and three vicariance events in the immediate ancestry of New World species; reconstructions for another four lineages were ambiguous. CONCLUSIONS New World Dryopteris are not monophyletic; vicariance has dominated the history of the North American species, while long-distance dispersal prevails in the Central and South American species, a pattern not previously seen in plants.
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Affiliation(s)
- Emily B Sessa
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin 53706, USA.
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Le Péchon T, Dubuisson JY, Haevermans T, Cruaud C, Couloux A, Gigord LDB. Multiple colonizations from Madagascar and converged acquisition of dioecy in the Mascarene Dombeyoideae (Malvaceae) as inferred from chloroplast and nuclear DNA sequence analyses. ANNALS OF BOTANY 2010; 106:343-57. [PMID: 20562131 PMCID: PMC2908169 DOI: 10.1093/aob/mcq116] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS In the Mascarenes, a young oceanic archipelago composed of three main islands, the Dombeyoideae (Malvaceae) have diversified extensively with a high endemism rate. With the exception of the genus Trochetia, Mascarene Dombeyoideae are described as dioecious whereas Malagasy and African species are considered to be monocline, species with individuals bearing hermaphrodite/perfect flowers. In this study, the phylogenetic relationships were reconstructed to clarify the taxonomy, understand the phylogeographic pattern of relationships and infer the evolution of the breeding systems for the Mascarenes Dombeyoideae. METHODS Parsimony and Bayesian analysis of four DNA markers (ITS, rpl16 intron and two intergenic spacers trnQ-rsp16 and psbM-trnD) was used. The molecular matrix comprised 2985 characters and 48 taxa. The Bayesian phylogeny was used to infer phylogeographical hypotheses and the evolution of breeding systems. KEY RESULTS Parsimony and Bayesian trees produced similar results. The Dombeyoideae from the Mascarenes are polyphyletic and distributed among four clades. Species of Dombeya, Trochetia and Ruizia are nested in the same clade, which implies the paraphyly of Dombeya. Additionally, it is shown that each of the four clades has an independent Malagasy origin. Two adaptive radiation events have occurred within two endemic lineages of the Mascarenes. The polyphyly of the Mascarene Dombeyoideae suggests at least three independent acquisitions of dioecy. CONCLUSIONS This molecular phylogeny highlights the taxonomic issues within the Dombeyoideae. Indeed, the limits and distinctions of the genera Dombeya, Trochetia and Ruizia should be reconsidered. The close phylogeographic relationships between the flora of the Mascarenes and Madagascar are confirmed. Despite their independent origins and a distinct evolutionary history, each endemic clade has developed a different breeding systems (dioecy) compared with the Malagasy Dombeyoideae. Sex separation appears as an evolutionary convergence and may be the consequence of selective pressures particular to insular environments.
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Affiliation(s)
- Timothée Le Péchon
- Université Pierre et Marie Curie, UMR CNRS-MNHN-UPMC "Centre de Recherche sur la Paléobiodiversité et les Paléoenvironnements", Paris, France.
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Zeng CX, Zhang YX, Triplett JK, Yang JB, Li DZ. Large multi-locus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals ten major lineages and low rate of molecular divergence. Mol Phylogenet Evol 2010; 56:821-39. [DOI: 10.1016/j.ympev.2010.03.041] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 03/31/2010] [Accepted: 03/31/2010] [Indexed: 11/24/2022]
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Li CX, Lu SG, Barrington DS. Phylogeny of Chinese Polystichum (Dryopteridaceae) based on chloroplast DNA sequence data (trnL-F and rps4-trnS). JOURNAL OF PLANT RESEARCH 2008; 121:19-26. [PMID: 18000642 DOI: 10.1007/s10265-007-0120-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 09/27/2007] [Indexed: 05/25/2023]
Abstract
Polystichum is one of the largest and most taxonomically complex fern genera in China. The evolutionary relationships of Chinese Polystichum and related genera, and the relationship between our Polystichum phylogeny and ecogeographic distribution, were tested by the use of DNA sequence data. Fifty-one species of Polystichum and 21 species in allied genera were sequenced for the plastid intergenic spacers rps4-trnS and trnL-F. Maximum parsimony and Bayesian phylogenetic analyses of both individual and combined data sets showed that Chinese Polystichum as commonly recognized was paraphyletic: one clade (the CCPC clade) included Cyrtomidictyum lepidocaulon, two Cyrtogonellum species, three Cyrtomium species, and a small number of Polystichum species usually occurring on limestone. A second clade, Polystichum sensu stricto, included the remainder of the Polystichum species; these often occur on non-limestone substrates. The remaining Cyrtomium species formed the third clade. Three subclades resolved within Polystichum sensu stricto (s.s.) clade do not correspond with recent sectional classifications, and we outline the issues relevant to a new classification for the genus.
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Affiliation(s)
- Chun-Xiang Li
- State Key Laboratory of Palaeobiology and Stratigraphy of the Nanjing Institute of Geology and Palaeontology, The Chinese Academy of Science, Nanjing, Jiangsu Province 210008, China.
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Simmons MP, Müller K, Norton AP. The relative performance of indel-coding methods in simulations. Mol Phylogenet Evol 2007; 44:724-40. [PMID: 17512758 DOI: 10.1016/j.ympev.2007.04.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 04/02/2007] [Accepted: 04/04/2007] [Indexed: 11/26/2022]
Abstract
We used simulations to compare the performance of 10 approaches that have been used for treating unambiguously aligned gaps in phylogenetic analyses. We examined how these approaches perform under the ideal conditions of correct alignments, as well as how robust they are to errors caused by use of inferred alignments. Our results indicate that 5th-state coding dramatically outperformed all other coding methods, which in turn all outperformed treating gaps as missing data or excluding gapped positions. Simple indel coding (SIC) and modified complex indel coding (MCIC) performed about the same, and generally outperformed the other indel-coding methods. The high performance of 5th-state coding was largely found to be a weighting artifact. We suggest that MCIC-coded gap characters be scored for all unambiguously aligned gaps in parsimony-based molecular phylogenetic analyses. When the number of terminals sampled precludes the use of MCIC, SIC may be used as an effective substitute.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO 80523-1878, USA.
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Li CX, Lu SG. Phylogenetics of Chinese Dryopteris (Dryopteridaceae) based on the chloroplast rps4-trnS sequence data. JOURNAL OF PLANT RESEARCH 2006; 119:589-98. [PMID: 16983488 DOI: 10.1007/s10265-006-0003-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Accepted: 04/13/2006] [Indexed: 05/11/2023]
Abstract
Dryopteris is one of the largest and most taxonomically complex fern genera in the Dryopteridaceae, with 127 species occurring throughout temperate, sub-temperate, subtropical, and tropical China. Investigations of the evolutionary relationships of a subset of these Chinese Dryopteris species, using DNA sequence-based methods, specifically tested the monophyly of the genus and the validity of the previous subgeneric classifications. Sixty species of Dryopteris, four closely related non-Dryopteris and three species of Arachniodes, were used as outgroup taxa. The rps4-trnS region of the chloroplast genome was sequenced in these species for the first time. Both maximum parsimony (MP) and neighbor-joining (NJ) analyses identified six polyphyletic clades that contained Dryopteris species. These results were supported by a Bayesian analysis of the same data set. The phylogenetic patterns strongly suggest the polyphyletic status of Dryopteris; the monophyletic groupings of the species do not correspond with either Fraser-Jenkins [In: Bull Brit Mus (Nat Hist) Bot 14(3):183-218, 1986} or Wu (In: Flora Reipublica Popularis Sinicae Tomus 5 (1) pp 1-241, 2000] subgeneric classification of Dryopteris, except in a few specific cases. This work represents the first molecular systematic analyses of Chinese Dryopteris, and we propose the next steps necessary to recognize new subgenera of the genus.
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Affiliation(s)
- Chun-Xiang Li
- State Key Laboratory of Palaeobiology and Stratigraphy of the Nanjing Institute of Geology and Palaeontology, Chinese Academy of Science, Nanjing, Jiangsu Province, People's Republic of China.
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Korall P, Pryer KM, Metzgar JS, Schneider H, Conant DS. Tree ferns: monophyletic groups and their relationships as revealed by four protein-coding plastid loci. Mol Phylogenet Evol 2006; 39:830-45. [PMID: 16481203 DOI: 10.1016/j.ympev.2006.01.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Revised: 12/22/2005] [Accepted: 01/02/2006] [Indexed: 11/22/2022]
Abstract
Tree ferns are a well-established clade within leptosporangiate ferns. Most of the 600 species (in seven families and 13 genera) are arborescent, but considerable morphological variability exists, spanning the giant scaly tree ferns (Cyatheaceae), the low, erect plants (Plagiogyriaceae), and the diminutive endemics of the Guayana Highlands (Hymenophyllopsidaceae). In this study, we investigate phylogenetic relationships within tree ferns based on analyses of four protein-coding, plastid loci (atpA, atpB, rbcL, and rps4). Our results reveal four well-supported clades, with genera of Dicksoniaceae (sensu ) interspersed among them: (A) (Loxomataceae, (Culcita, Plagiogyriaceae)), (B) (Calochlaena, (Dicksonia, Lophosoriaceae)), (C) Cibotium, and (D) Cyatheaceae, with Hymenophyllopsidaceae nested within. How these four groups are related to one other, to Thyrsopteris, or to Metaxyaceae is weakly supported. Our results show that Dicksoniaceae and Cyatheaceae, as currently recognised, are not monophyletic and new circumscriptions for these families are needed.
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Affiliation(s)
- Petra Korall
- Department of Biology, Duke University, Durham, NC 27708, USA.
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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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