Systematics of peninsular Malaysian scaly tree ferns (Cyatheaceae): phylogenetics, computer-aided identification and conservation

The work presented in this thesis evaluates the status of Peninsular MalaysianCyatheaceae and used molecular and morphological identification tools for the localspecies. 419 Cyatheaceae frond sample were collected from the widest possible rangeof Peninsular Malaysia to obtain material for morphology...

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Main Author:	Azi Azeyanty Jamaludin
Format:	thesis
Language:	eng
Published:	2017
Subjects:	QK Botany
Online Access:	https://ir.upsi.edu.my/detailsg.php?det=5362
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language	eng
topic	QK Botany
spellingShingle	QK Botany Azi Azeyanty Jamaludin Systematics of peninsular Malaysian scaly tree ferns (Cyatheaceae): phylogenetics, computer-aided identification and conservation
description	The work presented in this thesis evaluates the status of Peninsular MalaysianCyatheaceae and used molecular and morphological identification tools for the localspecies. 419 Cyatheaceae frond sample were collected from the widest possible rangeof Peninsular Malaysia to obtain material for morphology and molecular study. 15Cyathea species were identified and the species information for Peninsular Malaysiawas updated. The species was incorporated into the existing Cyatheaceae phylogenyby using four plastid regions: matK, rbcL, trnG-trnR and trnL-trnF. Bayesian MCMCanalysis of the concatenated sequence data resulted in a 50% majority rule consensustree confirm the placement of the four groups: Cyathea, Alsophila, Gymnosphaeraand Sphaeropteris in the family. However, the resulting tree representing nestedmonophyletic groups, proposing Cyatheaceae to be monogeneric, i.e., Cyathea withtwo large groups: Cyathea and Sphaeropteris. The same plastid regions were thenevaluated to develop DNA barcodes. trnL-trnF was proposed as a barcode for thisfamily as it almost satisfied the three most important criteria: primer universality,sequence quality and species discrimination. This research also developed a multiaccesskey for Cyatheaceae field identification based on fifteen taxa identified, byextensive field sampling of the currently recognised species. All of the Cyatheaceaespecies recognises in this study had also been assessed for the conservation statusbased on the IUCN Red List criteria. Nine species fall under Least Concern (LC), fourspecies are Near Threatened (NT) and two species are Vulnerable (VU). The thoroughknowledge regarding Cyatheaceae in Peninsular Malaysia gained through the workdone in this research will benefit in making appropriate conservation strategies for thesurvival of this family. Overall, the most important outcome of this research was thecombination of morphology and molecular data for the purpose of updatingtaxonomy, identification and conservation of the Cyatheaceae family in PeninsularMalaysia
format	thesis
qualification_name
qualification_level	Doctorate
author	Azi Azeyanty Jamaludin
author_facet	Azi Azeyanty Jamaludin
author_sort	Azi Azeyanty Jamaludin
title	Systematics of peninsular Malaysian scaly tree ferns (Cyatheaceae): phylogenetics, computer-aided identification and conservation
title_short	Systematics of peninsular Malaysian scaly tree ferns (Cyatheaceae): phylogenetics, computer-aided identification and conservation
title_full	Systematics of peninsular Malaysian scaly tree ferns (Cyatheaceae): phylogenetics, computer-aided identification and conservation
title_fullStr	Systematics of peninsular Malaysian scaly tree ferns (Cyatheaceae): phylogenetics, computer-aided identification and conservation
title_full_unstemmed	Systematics of peninsular Malaysian scaly tree ferns (Cyatheaceae): phylogenetics, computer-aided identification and conservation
title_sort	systematics of peninsular malaysian scaly tree ferns (cyatheaceae): phylogenetics, computer-aided identification and conservation
granting_institution	Universiti Pendidikan Sultan Idris
granting_department	Fakulti Sains Kemanusiaan
publishDate	2017
url	https://ir.upsi.edu.my/detailsg.php?det=5362
_version_	1747833183336923136
spelling	oai:ir.upsi.edu.my:53622020-11-16 Systematics of peninsular Malaysian scaly tree ferns (Cyatheaceae): phylogenetics, computer-aided identification and conservation 2017 Azi Azeyanty Jamaludin QK Botany The work presented in this thesis evaluates the status of Peninsular MalaysianCyatheaceae and used molecular and morphological identification tools for the localspecies. 419 Cyatheaceae frond sample were collected from the widest possible rangeof Peninsular Malaysia to obtain material for morphology and molecular study. 15Cyathea species were identified and the species information for Peninsular Malaysiawas updated. The species was incorporated into the existing Cyatheaceae phylogenyby using four plastid regions: matK, rbcL, trnG-trnR and trnL-trnF. Bayesian MCMCanalysis of the concatenated sequence data resulted in a 50% majority rule consensustree confirm the placement of the four groups: Cyathea, Alsophila, Gymnosphaeraand Sphaeropteris in the family. However, the resulting tree representing nestedmonophyletic groups, proposing Cyatheaceae to be monogeneric, i.e., Cyathea withtwo large groups: Cyathea and Sphaeropteris. The same plastid regions were thenevaluated to develop DNA barcodes. trnL-trnF was proposed as a barcode for thisfamily as it almost satisfied the three most important criteria: primer universality,sequence quality and species discrimination. This research also developed a multiaccesskey for Cyatheaceae field identification based on fifteen taxa identified, byextensive field sampling of the currently recognised species. All of the Cyatheaceaespecies recognises in this study had also been assessed for the conservation statusbased on the IUCN Red List criteria. Nine species fall under Least Concern (LC), fourspecies are Near Threatened (NT) and two species are Vulnerable (VU). The thoroughknowledge regarding Cyatheaceae in Peninsular Malaysia gained through the workdone in this research will benefit in making appropriate conservation strategies for thesurvival of this family. Overall, the most important outcome of this research was thecombination of morphology and molecular data for the purpose of updatingtaxonomy, identification and conservation of the Cyatheaceae family in PeninsularMalaysia 2017 thesis https://ir.upsi.edu.my/detailsg.php?det=5362 https://ir.upsi.edu.my/detailsg.php?det=5362 text eng closedAccess Doctoral Universiti Pendidikan Sultan Idris Fakulti Sains Kemanusiaan Abramoff, M.D., Magalhaes, P.J., Ram, S.J. (2004) Image processing with imageJ.Biophotonics International. (11), 36--42.Alvarez, I., Wendel, J.F. (2003) Ribosomal ITS sequences and plant phylogeneticinference. Molecular Phylogenetics and Evolution. 29(3), 417-434.Ashton, D.H. (2000) The Big Ash forest, Wallaby Creek, Victoria: changes during onelifetime. Australian Journal of Botany. 48, 1-26.Bachman, S., Moat, J., Hill, A.W., de Torre, J., Scott, B. (2011) Supporting Red List threatassessments with GeoCAT: geospatial conservation assessment tool. Zookeys. (150), 117-126.Bidin, A. (1987) A preliminary survey of the fern flora of Langkawi Islands. Garden BulletinSingapore. 40(2), 77-102.Bidin, A. (1983) Notes on the ferns and fern-allies of Carey Island. MalayanNaturalist. 37(1), 13-19.Bidin, A. (1985) The fern of the genus Brainea in Peninsular Malaysia. NatureMalaysiana. 10(2), 26-28.Bidin, A.A., Jaman, R. (1999) The Pteridophytes OfTawau Hills Park, Sabah. ASEAN Review ofBiodiversity and Environmental Conservation (ARBEC). (2), 11.Blows, M.W., Schwarz, M.P. (1991) Spatial-distribution of a primitively social bee: doesgenetic population structure facilitate altruism? . Evolution. 45(3), 680- 693.CBOL, P.W.G. (2009) A DNA barcode for land plants. Proceedings of the National Academy ofSciences. 106(31), 12794-12797.Chase, M.W., Fay, M.F. (2009) Ecology. Barcoding of plants and fungi. Science.325(5941), 682-683.Chen, C.W., Huang, Y.M., Kuo, L.Y., Nguyen, Q.D., Luu, H.T., Callado, J.R., Farrar, D.R., Chiou,W.L. (2013) trnL-F is a powerful marker for DNA identification of field vittarioid gametophytes(Pteridaceae). Ann Bot. 111(4), 663-673.Christenhusz, M.J., Chase, M.W. (2014) Trends and concepts in fern classification.Annals of Botany. 113(4), 571-594.Christenhusz, M.J.M., Zhang, X.-C., Schneider, H. (2011) A linear sequence of extant families andgenera of lycophytes and ferns. Phytotaxa. 19, 7-54.Christensen, C. (1905) Index Filicum. Copenhagen: Hagerup.Cicuzza, D. (2014) A rediscovery of Alfred Russel Wallace's fern collection fromBorneo at the Cambridge University Herbarium. Notes and Records: the Royal Society journal of thehistory of science. 68(4), 403-412.CITES (2013) The CITES Appendices.. (28/03/2016). [online]. Available from:https://cites.org/eng/app/index.php.Conant, D.S., Raubeson, L.A., Attwood, D.K., Stein, D.B. (1995) The Relationships of PapuasianCyatheaceae to New World Tree Ferns. American Fern Journal. 85(4), 328-340.Conant, D.S., Stein, D.B. (2001) Phylogenetic and geographic relationships of the tree ferns(Cyatheaceae) on Mount Kinabalu. Sabah Parks Nature Journal. 4(25- 43).Conant, D.S., Stein, D.B., Valinski, A.E.C., Sudarsanam, P., Ahearn, M.E. (I 994)Phylogenetic Implications of Chloroplast DNA Variation in the Cyatheaceae.I. Systematic Botany. 19(1), 60-72.DNASTAR (2016) SeqMan Pro.Dong, W., Cheng, T., Li, C., Xu, C., Long, P., Chen, C., Zhou, S. (2014) Discriminating plants using the DNA barcode rbcLb: an appraisal based on a large dataset. Mo/ Ecol Resour. 14(2), 336-343.Doyle, J.J., Doyle, J.L. (1987) A rapid DNA isolation procedure for small quantities offresh leaf tissue. Phychem Bull. 19, 11-15.Drew, L.W. (2011) Are We Losing the Science of Taxonomy? BioScience. 61(12), 942-946.Duffy, A.M., Kelchner, S.A., Wolf, P.G. (2009) Conservation of selection on matK followingan ancient loss of its flanking intron. Gene. 438(1-2), 17-25.Ebihara, A., Nitta, J.H., Ito, M. (2010) Molecular species identification with richfloristic sampling: DNA barcoding the pteridophyte flora of Japan. PLoS One. 5(12), el 5136.Erickson, D.L., Spouge, J., Resch, A., Weigt, L.A., Kress, W.J. (2008) DNABarcoding in land plants: developing standards to quantify and maximize success. Taxon.(57), 1304-1316.Ferri, G., Corradini, B., Ferrari, F., Santunione, A.L., Palazzoli, F., Alu, M. (2015)Forensic botany II, DNA barcode for land plants: Which markers after the internationalagreement? Forensic Sci Int Genet. 15, 131-136.Fountain-Jones, N.M., McQuillan, P.B., Grove, S. (2012) Beetle communitiesassociated with the tree fern Dicksonia antarctica Labill. in Tasmania.Australian Journal of Entomology. 51(3), 154-165.Fraser-Jenkins, C.R. (2009) A brief comparison of modern pteridophyte classifications (families andgenera in India). Indian Fern Journal. (26), 107-126.FRIM, F.R.I.M. (2013) Biological Diversity Clearing House Mechanism: FloraDatabase.Gastony, G.J., Yatskievych, G. (1992) Maternal inheritance of the chloroplast andmitochondrial genomes in cheilanthoid ferns. American Journal of Botany.(79),716-722.Giudicelli, G.C., M??der, G., de Freitas, L.B. (2015) Efficiency of ITS sequences forDNA barcoding in Passiflora (Passifloraceae). International Journal ofMolecular Sciences. 16(4), 7289-7303.Grayer, S. (2009) The Royal Horticultural Society's Colour Chart: an everyday toolfor use in the herbarium. Its past, present and future. Natural SciencesCollections Association. (18), 19-26.de Groot, G.A., During, H.J., Maas, J.W., Schneider, H., Vogel, J.C., Erkens, R.H.(2011) Use ofrbcL and trnL-F as a two-locus DNA barcode for identificationofNW-European ferns: an ecological perspective. PLoS One. 6(1), el6371.Hall, R. (1998) The Plate Tectonics Of Cenozoic Se Asia And The Distribution OfLand And Sea. In R Hall & J. D. Holloway, eds. Biogeography andGeological Evolution of SE Asia. Leiden, The Netherlands: BackhuysPublishers.Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor andanalysis program for windows 95/98/NT. Nucleic Acids Symposium. (41),95-98.Hartvig, I., Czako, M., Kjaer, E.D., Nielsen, L.R, Theilade, I. (2015) The use of ON Abarcoding in identification and conservation of rosewood (Dalbergia spp.).PLoS One. (10), e0138231.Hasebe, M., Omori, T., Nakazawa, M., Sano, T., Kato, M., Iwatsuki, K (1994) rbcLGene Sequences Provide Evidence for the Evolutionary Lineages ofLeptosporangiate Ferns. Proceedings of the National Academy of Science ofthe United States ofAmerica. 91(12), 5730-5734.Hasebe, M., Wolf, P.G., Pryer, KM., Ueda, K, Ito, M., Sano, R., Gastony, GJ.,Yokoyama, J., Manhart, J.R., Murakami, N., Crane, E.H., Haufler, C.H., Hauk,W.D. (1995) Fern Phylogeny Based on rbcL Nucleotide Sequences. AmericanFern Journal. 85(4),134-181.Hebert, P.D., Cywinska, A., Ball, S.L., deWaard, J.R (2003) Biologicalidentifications through DNA barcodes. Proc Bioi Sci. 270(1512), 313-321.Hebert, P.D., Gregory, T.R. (2005) The promise of DNA barcoding for taxonomy ..(54),852-859.Hebert, P.D., Penton, E.H., Burns, J.M., Janzen, D.H., Hallwachs, W. (2004) Tenspecies in one: DNA barcoding reveals cryptic species in the neotropicalskipper butterfly Astraptes fulgerator. Proc Nat! Acad Sci USA. 101(41),14812-14817.Hebert, P.D., Stoeckle, M.Y., Zemlak, T.S., Francis, C.M. (2004) Identification of Birdsthrough DNA Barcodes. PLoS Biol. 2( 10), e3 l 2.Hollingsworth, M.L., Andra Clark, A., Forrest, L.L., Richardson, J., Pennington, R.T., Long,D.G., Cowan, R., Chase, M.W., Gaudeul, M., Hollingsworth, P.M. (2009) Selectingbarcoding loci for plants: evaluation of seven candidate loci with species-level samplingin three divergent groups of land plants. Mo! Ecol Resour. 9(2), 439-457.Hollingsworth, P.M. (2011) Refining the DNA barcode for land plants. Proceedings of theNational Academy of Sciences. 108(49), 19451-19452.Hollingsworth, P.M., Graham, S.W., Little, D.P. (2011) Choosing and using a plant DNAbarcode. PLoS ONE. 6(5).Holttum, R.E. (1968) A Revised Flora of Malaya. Fern of Malaya 2. Singapore: SingaporeGovt. Printing Office.Holttum, R.E. (1963) Cyatheaceae. In C. G. G. J. Van Steenis & R. E. Holttum, eds.Flora Malesiana Series JI-Pteridophyta: Fern and Fern Allies. Volume 1 Part2. Netherlands: Martinus Nijhoff/Dr W. Junk Publishers.Holttum, R.E. (1966) New Fems from Malesia. Kew Bulletin. 20(3), 6.Holttum, R.E. (1964) The Genus Cyathea (sensu Jato) in Malaysia. American Fern Journal.54(1), 9.Holttum, R.E. (1957) The Scales of Cyatheaceae. (With Special Reference to the GenusSchizocaena J. Sm.). Kew Bulletin. 12(1), 5.Holttum, R.E., Edwards, P.J. (1983) The Tree-Fems of Mount Roraima andNeighbouring Areas of the Guayana Highlands with Comments on the Family Cyatheaceae. KewBulletin. 38(2), 155-188.IUCN (2015) The IUCN Red List of Threatened Species. Version 2015-4.Jaman, R., Latiff, A. (1998) On Some Pteridophytes of Sayap-Kinabalu Park, Sabah.ASEAN Review of Biodiversity and Environmental Conservation (ARBEC), 35.Jaman, R., Latiff, A. (1999) The Pteridophyte Flora Of Pulau Tioman, PeninsularMalaysia. The Raffles Bulletin Of Zoology. 6, 24.Kane, N.C., Cronk, Q. (2008) Botany without borders: barcoding in focus. Mo! Ecol.17(24), 5175-5176.Konyves, K. (2014) Taxonomy To Underpin Cultivar Identification In Hoop-Petticoat Daffodils.University of Reading.Korall, P., Conant, D.S., Metzgar, J.S., Schneider, H., Pryer, K.M. (2007) A molecular phylogenyof scaly tree fems (Cyatheaceae). American Journal of Botany. 94(5), 873-886.Korall, P., Pryer, K.M. (2014) Global biogeography of scaly tree fems (Cyatheaceae): evidence for Gondwanan vicariance and limited transoceanic dispersal. J Biogeogr. 41(2),402-413.Korall, P., Pryer, K.M., Metzgar, J.S., Schneider, H., Conant, D.S. (2006) Tree fems:monophyletic groups and their relationships as revealed by four protein-coding plastid loci.Molecular Phylogenetics and Evolution. 39(3), 830-845.Kramer, K.U. (1990) Cyatheaceae. In K. U. Kramer & P. S. Green, eds. Pteridophytes andGymnosperms: The Families and Genera of Vascular Plants Volume I. Berlin: Springer-Verlag,pp. 69-74.Kress, W.J., Erickson, D.L. (2008) DNA barcodes: genes, genomics, andbioinformatics. Proc Natl Acad Sci US A. 105(8), 2761-2762.Kress, W.J., Wurdack, K.J., Zimmer, E.A., Weigt, L.A., Janzen, D.H. (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci U S A. 102(23), 8369-8374.Kuo, L.Y., Li, F.W., Chiou, W.L., Wang, C.N. (2011) First insights into fern matKphylogeny. Mo/ Phylogenet Evol. 59(3), 556-566.Lahaye, R., van der Bank, M., Bogarin, D., Warner, J., Pupulin, F., Gigot, G., Maurin, 0.,Duthoit, S., Barraclough, T.G., Savolainen, V. (2008) DNA barcoding the floras ofbiodiversity hotspots. Proc Natl Acad Sci US A. 105(8), 2923-2928.Large, M.F., Braggins, J.E. (2004) Tree Ferns. Cambridge: Timber Press.Latiff, A. (2015) Cyathea arjae Latiff (Cyatheaceae), A New Species of Dwarf Tree Fem fromSayap, Mt. Kinabalu, Sabah, Malaysia. Sains Malaysiana. 44(1 ), 4.Lee, S.S., Swanson, E., Abuzeid, A., Akhlaghi, M., Amjadi, A., Batjargal, U.,Cieslikowski, D., Dookhony, L., Fix, R., Hatakeyama, S., Hiraga, M., Horiuchi,K., Kalimili, B.B.N., Khaltarkhuu, B.E., Kwong, A., Lateef, K.S., Levent, I., Muhula,R., Sun, C., Vijayalakshmi, K.M., Zamora, E., Group, D.E.V.P.D.D., Bank, T.W. (2010) World Development Indicators. M. de Coquereaumont, B. Ross-Larson, & C. Trott, eds.Washington, USA: The World Bank.Lehnert, M. (2006) New species and records of tree fems (Cyatheaceae, Pteridophyta) from thenorthern Andes. Organisms Diversity & Evolution. 6(4), 321-322.Lehnert, M. (2009) Three new species of scaly tree fems (Cyathea-Cyatheaceae) from the northernAndes. Phytotaxa. 1, 43-56.Lehtonen, S. (2011) Towards resolving the complete fem tree of life. PLoS One.6(10), e2485 l.Lellinger, D.B. (1987) The Disposition ofTrichopteris (Cyatheaceae). American Fern Journal.77(3), 90-94.Li, F.-W., Tan, B.C., Buchbender, V., Moran, R.C., Rouhan, G., Wang, C.-N.,Quandt, D. (2009) Identifying a mysterious aquatic fem gametophyte. Plant Systematics andEvolution. 281(1-4), 77-86.Li, F.W., Kuo, L.Y., Rothfels, C.J., Ebihara, A., Chiou, W.L., Windham, M.D., Pryer,K.M. (2011) rbcL and matK earn two thumbs up as the core DNA barcode for ferns. PLoS One. 6(10),e26597.Li, X., Yang, Y., Henry, R.J., Rossetto, M., Wang, Y., Chen, S. (2015) Plant DNAbarcoding: from gene to genome. Biol Rev Camb Philos Soc. 90(1), 157-166.Liao, Y.Y., Yang, X.Y., Motley, T.J., Chen, J.M., Wang, Q.F. (201 I)Phylogeographic analysis reveals two cryptic species of the endangered fern Ceratopteristhalictroides (L.) Brongn. (Parkeriaceae) in China. Conservation Genetics. 12(5), 1357-1365.Lindenmayer, D.B., Cunningham, R.B., Donnelly, C.F., Triggs, B.J., Belvedere, M. (1994)The conservation of arboreal marsupials in the montane ash forests of the central highlandsof Victoria, South-Eastern Australia V. Patterns of use and the microhabitat requirements of the mountain brushtail possum Trichosurus caninus ogilby inretained I. Biological Conservation. 68( I), 43- 51.Lindsay, S., Middleton, D.J. (2009) Development of a multi-access key to the ferns of Thailand.THAI FOR. BULL. (BOT.), 4.Ma, K. (2010) The First Asian Plant Conservation Report. Beijing, China.Ma, X.-Y., Xie, C.-X., Liu, C., Song, J.-Y., Yao, H., Luo, K., Zhu, Y.-J., Gao, T.,Pang, X.-H., Qian, J., Chen, S.-L. (2010) Species Identification of Medic inal Pteridophytes by a DNA Barcode Marker, the Chloroplast psbA-trnH lntergenic Region.Pharmaceutical Society of Japan. 33(1 I), 6.Meier, R., Shiyang, K., Vaidya, G., Ng, P.K.L. (2006) DNA Barcoding andTaxonomy in Diptera: A Tale of High Intraspecific Variability and Low IdentificationSuccess. Syst Biol. 55(5), 715-728.Metcalfe, I. (2002) Permian Tectonic Framework and Paleogeography of SE Asia.Journal of Asian Earth Science. 20, 551-566.MNRE (2014) 5th Report to Convention On Biological Diversity. B. and F. M. Division,ed. Kuala Lumpur, Malaysia: The Government of Malaysia.MNRE (2006) Biodiversity in Malaysia C. and E. M. Division, ed. MultilateralEnvironmental Agreements: Capacity Building and Implementation Project.MNRE (2016) National Policy On Biological Diversity 2016-2025. Putrajaya, Malaysia:The Ministry of Natural Resources and Environment.MSET (1998) Malaysia's National Policy on Biological Diversity E. and T. Ministry of Science,ed., 27.Nagalingum, N.S., Schneider, H., Pryer, K.M. (2007) Molecular PhylogeneticRelationships and Morphological Evolution in the Heterosporous Fern Genus Marsilea.Systematic Botany. 32(1), 16-25.Napis, S., Mat Salleh, K., Itam, K., Latiff, A. (2001) Biodiversity databases forMalaysian Flora and Fauna: an update. In Proceedings of Internet Workshop 2001. NationalInstitute oflnformatics, Tokyo, Japan.Nock, C.J., Waters, D.L., Edwards, M.A., Bowen, S.G., Rice, N., Cordeiro, G.M., Henry,R.J. (2011) Chloroplast genome sequences from total DNA for plant identification. PlantBiotechnology Journal. (9), 328-333.Norton, G. (2000) Invasive Species: The Role Of Lucid Identification Keys.Proceedings of International Seminar on Biological Invasions., 4.Nunes, C.F., Ferreira, J.L., Nunes Fernandes, M.C., Breves, S.D.S., Generoso, a. L., FontesSoares, B.D., Carvalho Dias, M.S., Pasqual, M., Borem, a., Almeida Cam;ado, G.M. (2011)Otimiza9ao de um metodo para extra9ao de DNA genomico a partir de folhas de morangueiro.Ciencia Rural. 41(8), 1383-1389.Nylander, J. (2004) MrModeltest, Version 2.Oldfield, S. (1995) International Trade of Tree-Ferns and Evaluation on theApplication of CITES. Cambridge: World Conservation Monitoring Centre.Parris, B.S., Latiff, A. (1997) Towards a pteridophyte flora of Malaysia: a provisional checklistoftaxa. Malayan Nature Journal. 50, 235-280.Pichi-Sermolli, R.E.G. (1973) Historical review of the higher classification of theFilicopsida. In: JERMY, A. C., CRABBE, J. A. & THOMAS, B. A. (eds.).Botanical Journal Linnean Society.Piggott, A.G. (1988) Ferns of Malaysia in Colour. Kuala Lumpur: Tropical Press Sdn.Bhd.Pryer, K.M., Schneider, H., Smith, A.R., Cranfill, R., Wolf, P.G., Hunt, J.S., Sipes,S.D. (2001) Horsetails and ferns are a monophyletic group and the closest livingrelatives to seed plants. Nature. 409, 618--622.Pryer, K.M., Schuettpelz, E., Huiet, L., Grusz, A.L., Rothfels, C.J., Avent, T., Schwartz, D., Windham, M.D. (2010) DNA barcoding exposes a case of mistakenidentity in the fern horticultural trade. Mal Ecol Resour. 10(6), 979- 985.Pryer, K.M., Schuettpelz, E., Wolf, P.G., Schneider, H., Smith, A.R., Cranfill, R.(2004) Phylogeny And Evolution Of Ferns (Monilophytes) With A Focus On The EarlyLeptosporangiate Divergences. American Journal of Botany. 91(10), 17.Pryer, K.M., Smith, A.R., Skog, J.E. (1995) Phylogenetic Relationships of Extant FernsBased on Evidence from Morphology and rbcL Sequences. American Fern Journal. 85(4),205-282.Rambaut, A. (2014) FigTree vl.4.2.Rambaut, A., Suchard, M.A., Xie, D., Drummond, A.J. (2014) Tracer vi .6.Rankou, H., Culham, A., Taleb, M.S., Ouhammou, A., Martin, G., Jury, S.L. (2015)Conservation Assessments and Red Listing of The Endemic Moroccan Flora (Monocotyledons).Botanical Journal of the Linnean Society. 177, 504-575.Richmond, S. (2010) Malaysia, Singapore & Brunei. C. Brash, A. Karlin, S. Low, &B. Presser, eds. Lonely Planet.Ridley, H.N. (1912) A botanical survey of Pulau Adang. Journal of the Straits Branch of the RoyalAsiatic Society. 61, 45--65.Ridley, H.N. (1908) A List ofthe Ferns of the Malay Peninsula. Journal of the Straits Branch of theRoyal Asiatic Society. 50, 1-59.Ridley, H.N. (1926) Ferns of the Malay Peninsula. London: Reeves and Company Ltd.Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D.L., Darling, A., Hohna, S.,Larget, B., Liu, L., Suchard, M.A., Huelsenbeck, J.P. (2012) MrBayes 3.2: efficientBayesian phylogenetic inference and model choice across a large model space. Systematicbiology, 61, 539-542. Systematic Biology. (61), 539-542.Rothfels, C.J., Larsson, A., Kuo, L.Y., Korall, P., Chiou, W.L., Pryer, K.M. (2012)Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiationof eupolypod Ir ferns. Syst Biol. 61(3), 490-509.Rothfels, C.J., Sunduem, M.A., Kuo, L.-Y., Larsson, A., Kato, M., Schuettpelz, E.,Pryer, K.M. (2012) A revised family-level classification for eupolypod II ferns (Polypodiidae:Polypodiales). Taxon. 61(3), 515-533.Rout, S.D., Panda, T., Mishra, N. (2009) Ethnomedicinal studies on somepteridophytes of Similipal Biosphere Reserve, Orissa, India. International Journal ofMedicine and Medical Sciences. 1(5), I 92-197.Sanger, F., Coulson, A.R. (1975) A rapid method for determining sequences in DNA by primedsynthesis with DNA polymerase. Journal of Molecular Biology. (94), 441-448.Schneider, H., He, L., Hennequin, S., Zhang, X.-C. (2013) Towards a naturalclassification of Pteridaceae: inferring the relationships of enigmatic pteridoid fern speciesoccuring in the Sino-Himalaya and Afro-Madagascar. Phytotaxa. (77), 49--60.Schneider, H., Ranker, T.A., Russell, S.J., Cranfill, R., Geiger, J.M., Aguraiuja, R.,Wood, K.R., Grundmann, M., Kloberdanz, K., Vogel, J.C. (2005) Origin of the endemic fern genusDiellia coincides with the renewal of Hawaiian terrestrial life in the Miocene. Proc Biol Sci.272(1561 ), 455-460.Schneider, H., Schuettpelz, E. (2006) Identifying fem gametophytes using DNA sequences.Molecular Ecology Notes. 6(4), 989-991.Schuettpelz, E., Pryer, K.M. (2007) Fem Phylogeny Inferred from 400Leptosporangiate Species and Three Plastid Genes. Taxon. 56(4), I 037-1050.Secretariat of the Convention on Biological Diversity (2010) Global BiodiversityOutlook 3., 94.Smith, A.R., Pryer, K.M., Korall, P., Schneider, H., Wolf, P.O. (2006) A classification for extantfems. Taxon. 55(3), 705-731.Smith, A.R., Pryer, K.M., Schuettpelz, E., Korall, P. (2008) Fem Classification. In T.A. RANKER & C. H. HAUFLER, eds. Biology and evolution offerns and lycophytes. Cambridge:Cambridge University Press.Smith, S.Y., Rothwell, G.W., Stockey, R.A. (2003) Cyathea cranhamii sp. nov.(Cyatheaceae), anatomically preserved tree fem sori from the lower cretaceous of Vancouver island,British Columbia. American Journal of Botany. 90(5), 6.Sonet, G. (2013) DNA Barcoding Flies of Forensci Interest: Validation Test Using LocalEntomofauna. Barcode Bulletin. 4(2), 20.Stein, D.B., Conant, D.S., Valinski, A.E.C. (1997) The implications of chloroplast DNA restriction site variation on the classification and phylogeny of the Cyatheaceae R. J.Johns, ed. Holttum Memorial Volume.Sucher, N.J., Carles, M.C. (2008) Genome-based approaches to the authentication of medicinalplants. Planta Medica. (74), 603-623.Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T.,Corthier, G., Brochmann, C., Willerslev, E. (2007) Power and limitations of the chloroplasttrnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res. 35(3), el4.Taberlet, P., Gielly, L., Pautou, G., Bouvet, J. (1991) Universal primers foramplification of three non-coding regions of chloroplast DNA. Plant MolecularBiology. 17, 1105-1109.Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S. (2013) MEGA6: MolecularEvolutionary Genetics Analysis version 6.0. Mo/ Biol Evol. 30(12), 2725-2729.Tryon, R.M. (1952) A sketch of the history of fern classification. Annals of theMissouri Botanical Garden. (39), 255-262.Tryon, R.M. (1970) The classification of the Cyatheaceae. Contributions from the GrayHerbarium of Harvard University. 200, 3-53.Tryon, R.M., Gastony, G.J. (1975) The biogeography of endemism in theCyatheaceae. Fern Gazette. 11, 73-79.Tryon, R.M., Tryon, A.F. (1982) Fems and Allied Plants, with Special Reference to TropicalAmerica.Vaidya, G., Lohman, D.J., Meier, R. (201 I) SequenceMatrix: concatenation software for thefast assembly of multi-gene datasets with character set and codon information. Cladistics.27(2), 171-180.Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M., Barton, G.J. (2009) Jalview Version 2--a multiple sequence alignment editor and analysis workbench.Bioinformatics. 25(9), I 189-1191.Wiemers, M., Fiedler, K. (2007) Does the DNA barcoding gap exist? - a case study in bluebutterflies (Lepidoptera: Lycaenidae). Front Zoo!. (8), 8.Wolf, P.G., Sipes, S.D., White, M.R., Martines, M.L., Pryer, K.M., Smith, A.R., Ueda,K. (1999) Phylogenetic relationships of the enigmatic fem families Hymenophyllopsidaceaeand Lophosoriaceae: Evidence from rbcL nucleotide sequences. Plant Systematics and Evolution.(219), 263-270.Yang, J.-B., Tang, M., Li, H.-T., Zhang, Z.-R., Li, D.-Z. (2013) Complete chloroplast genome ofthe genus cymbidium: Lights into the species identification, phylogenetic implicationsand population genetic analyses. BMC Evolutionary Biology. (13), 1-12.

Systematics of peninsular Malaysian scaly tree ferns (Cyatheaceae): phylogenetics, computer-aided identification and conservation

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