Abstract
Taxonomy is a systematic classification of living organisms, whereas phylogeny is a theoretical model of the sequence of evolutionary divergence of organisms from their common ancestors. Phylogeny is derived from a combination of Greek words: phylon means stem and genesis means origin. It is the study of evolutionary relationships among organisms. Traditionally, morphology, anatomy, physiology, and paleontology are used to determine the phylogeny (Riley 2009). In Pandanaceae, the morphological characters used to describe species are mainly based on fruit. Further, characterization of the species requires a large set of phenotypic data that are difficult to access statistically and are variable due to environmental effects (Sedra et al. 1993, 1996, 1998). There are a number of DNA-based marker systems available for studying phylogeny. Unlike morphological markers, molecular markers are not prone to environmental influences and do portray the genetic relationship between plant groups (Powell 1992; Gottlieb 1977; Tanksley et al. 1989; McCouch and Tanksley 1991).
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References
Avise JC (1986) Mitochondrial DNA and the evolutionary genetics of higher animals. Philos Trans R Soc Lond B Biol Sci 312:325–342
Avise JC (1994) The real message from Biosphere 2. Conserv Biol 8:327–329
Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst 18:489–522
Bakker FT, Culham A, Daugherty LC, Gibby M (1999) A trnL-F based phylogeny for species of Pelargonium (Geraniaceae) with small chromosomes. Plant Syst Evol 216:309–324
Bayer RJ, Starr JR (1999) Tribal phylogeny of the Asteraceae based on two non-coding chloroplast sequences, the trnL intron and trnL/trnF intergenic spacer. Ann Missouri Bot Gard 85:242–256
Buerki S, Callmander MW, Devey DS, Chappell L, Gallaher T, Munzinger J, Haevermans T, Forest F (2012) Straightening out the screw-pines: a first step in understanding phylogenetic relationships within Pandanaceae. Taxon 61(5):1010–1020
Callmander MW, Chassot P, Kupfer P, Lowry PP (2003) Recognition of Martellidendron, a new genus of Pandanaceae, and its bio-geographic implication. Taxon 52:747–762
Callmander MW, Lowry PP II, Forest F, Devey DS, Beentje H, Buerki S (2012) Benstonea Callm. & Buerki (Pandanaceae): characterization, circumscription, and distribution of a new genus of screw-pines, with a synopsis of accepted species. Candollea 67(2):323–345
Cech TR (1988) Conserved sequences and structures of group I introns: building an active site for RNA catalysis – a review. Gene 73:259–271
Chase MW, Soltis DE, Olmstead RG, Morgan D, Les DH, Mishler BD, Duval MR, Price RA, Hills HG, Qiu Y-L, Kron KA, Rettig JH, Conti E, Palmer JD, Manhart JR, Sytsma KJ, Michael HJ, Kress WJ, Karol KG, Clark WD, Hedren M, Gaut BS, Jansen RK, Kim K-J, Wimpee CF, Smith JF, Furnier GR, Strauss SH, Xiang Q-Y, Plunkett GM, Soltis PS, Swensen SM, Williams SE, Gadek PA, Quinn CJ, Eguiarte LE, Golenberg E, Learn GH Jr, Graham SW, Barrett SCH, Dayanandan S, Albert VA (1993) Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Ann Missouri Bot Gard 80:528–580
Chiang TY, Schaal BA, Peng CI (1998) Universal primers for amplification and sequencing a noncoding spacer between the atpB and rbcL genes of chloroplast DNA. Bot Bull Acad Sin 39:245–250
Clegg MT, Zurawski G (1992) Chloroplast DNA and the study of plant phylogeny: present status and future prospects. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematic of plants. Chapman and Hall, New York
Compton JA, Culham A, Jury S (1998) Reclassification of Actaea to include Cimicifuga and Souliea (Ranunculaceae): phylogeny inferred from morphology, nrDNA ITS and cpDNA trnL-F sequence variation. Taxon 47:593–634
Doyle J, Doyle J (1987) A rapid DNA isolation procedure for small amount of fresh leaf tissue. Phytochem Bull 5:547–555
Efron B (1979) Bootstrap methods: another look at the jackknife. Ann Statist 7:1–26
Farris JS (1983) The logical basis of phylogenetic systematics. In: Platnick NI, Funk VA (eds) Advances in cladistics. Columbia University Press, New York, pp 7–36
Felsenstein J (1983) Parsimony in systematics: biological and statistical issues. Annu Rev Ecol Syst 14:313–333
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Felsenstein J (2004) PHYLIP (Phylogeny Inference Package) version 3.68. Department of Genetics, University of Washington, Seattle
Fitch WM (1971) Toward defining the course of evolution: minimal change for a specific tree topology. Syst Zool 20:406–416
Gottlieb LD (1977) Electrophoretic evidence and plant systematics. Ann Missouri Bot Gard 64:161–180
Hao B, Qi J (2003) Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. In: Proceedings of the 2003 IEEE bioinformatics conference, IEEE Computer Society Washington, DC, pp 375–385
Harrison RG (1989) Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol Evol 4:6–11
Henry AN, Chithra V, Balakrishnan AN (1989) Flora of Tamil Nadu, India, vol III, Series 1, Analysis. Botanical Survey of India, Southern Circle, Coimbatore, 54
Hillis DM, Wiens JJ (2000) Molecules versus morphology in systematics: conflicts, artifacts, and misconceptions. In: Wiens JJ (ed) Phylogenetic analysis of morphological data. Smithsonian Institution Press, Washington, DC, pp 1–19
Hillis DM, Moritz C, Mable BK (eds) (1996) Molecular systematics. Sinauer Associates, Inc., Sunderland
Hilu KW, Borsch T, Muller K, Soltis DE, Soltis PS, Savolainen V, Chase MW, Powell MP, Alice LA, Evans R, Sauquet H, Neinhuis C, Slotta TAB, Rohwer JG, Campbell CS, Chatrou LW (2003) Angiosperm phylogeny based on matK sequence information. Am J Bot 90:1758–1776
Holder M, Lewis PO (2003) Phylogeny estimation: traditional and Bayesian approaches. Nat Rev Genet 4:275–284
Huelsenbeck JP, Ronquist FR, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310–2314
Johnson LA, Soltis DE (1994) matK DNA-Sequences and phylogenetic reconstruction in Saxifragaceae S-Str. Syst Bot 19:143–156
Johnson LA, Soltis DE (1995) Phylogenetic inference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using matK sequences. Ann Missouri Bot Gard 82:149–175
Källersjö M, Farris JS, Chase MW, Bremer B, Fay MF, Humphries CJ, Petersen G, Seberg OL, Bremer K (1998) Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants. Plant Syst Evol 213:259–287
Karthikeyan SK, Jain SK, Nayar MP, Sanjappa M (1989) Flora of India, Series 4, Florae Indicae Enumeratio: Monocotyledonae. Botanical Survey of India, Calcutta, pp 177–178
Keller J (2001) Pandanaceae. In: Hanelt P, Institute of Plant Genetics and Crop Plant Research (eds) Mansfield’s encyclopedia of agricultural and horticultural crops, vol 5. Springer, Berlin, pp 2816–2824
Kim KJ, Jansen RK (1995) ndhF sequence evolution and the major clades in the sunflower family. Proc Natl Acad Sci USA 92:10379–10383
Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
Kranz HD, Huss VAR (1996) Molecular evolution of ferns and allies, and their relationship to seed plants: evidence from complete 18 S rRNA gene sequences. Plant Syst Evol 202:1–11
Kranz HD, Miks D, Siegler M-L, Capesius I, Sensen CHW, Huss VA (1995) The origin of land plants: phylogenetic relationships between Charophytes, Bryophytes, and vascular plants inferred from complete small subunit ribosomal RNA gene sequences. J Mol Evol 41:74–84
Larget B, Simon DL (1999) Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol Biol Evol 16:750–759
Manhart JR (1994) Phylogenetic analysis of green plant rbcL sequences. Mol Phyl Evol 3:114–127
Mauro DS, Agorreta A (2010) Molecular systematics: a synthesis of the common methods and the state of knowledge. Cell Mol Biol Lett 15:311–341
McCouch SR, Tanksley SD (1991) Development and use of restriction fragment length polymorphism in rice breeding and genetics. In: Khush GS, Toenniessen GH (eds) Rice biotechnology. CAB International and IRRI, Wallingford/Oxon/Manila, pp 109–133
McDade LA, Moody ML (1999) Phylogenetic relationships among Acanthaceae: evidence from non-coding trnL-trnF chloroplast DNA sequences. Am J Bot 86:70–80
Michel F, Dujon B (1983) Conservation of RNA secondary structures in two intron families including mitochondrial, chloroplast and nuclear-encoded members. EMBO J 2:33–38
Moritz C, Dowling TE, Brown WM (1987) Evolution of animal mitochondrial DNA relevance for population biology and systematics. Annu Rev Ecol Syst 18:269–292
National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov. Access on 26 Mar 2012
National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/GenBank. Access on 26 Mar 2012
Nickrent DL, Soltis DE (1995) A comparison of angiosperm phylogenies from nuclear 18 s rDNA and rbcL sequences. Ann Missouri Bot Gard 82:208–234
Olmstead RG, Reeves PA (1995) Evidence for the polyphyly of the Scrophulariaceae based on chloroplast rbcL and ndhF sequences. Ann Missouri Bot Gard 82:176–193
Palmer JD (1985a) Comparative organization of chloroplast genomes. Annual Rev Genet 19:325–354
Palmer JD (1985b) Chloroplast DNA and molecular phylogeny. Bioessays 2:263–267
Palmer JD (1992) Mitochondrial DNA in plant systematics: applications and limitations. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematics of plants. Chapman & Hall, New York, pp 36–49
Pirie MD, Vargas MPB, Botermans M, Bakker FT, Chatrou LW (2007) Ancient paralogy in the cpDNA trnL–F region in Annonaceae: implications for plant molecular systematics. Am J Bot 94:1003–1016
Powell W (1992) Plant genomes, gene markers and linkage maps. In: Moss JP (ed) Biotechnology and crop improvement in Asia. ICRISAT, Hyderabad, pp 297–322
Qiu YQ, Palmer JD (1998) Phylogeny of early land plants: insights from genes and genomes. Trends Plant Sci 4:26–30
Quandt D, Müller K, Stech M, Frahm J-P, Frey W, Hilu KW, Borsch T (2004) Molecular evolution of the chloroplast trnL-F region in land plants. Monogr Syst Bot Missouri Bot Gard 98:13–37
Rambaut A (2006) Figtree version 1.0, Institute of Evolutionary Biology, University of Edinburgh, UK. Available on http://tree.bio.ed.ac.uk/software/figtree/
Rannala B, Yang Z (1996) Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J Mol Evol 43:304–311
Reijmers TH, Wehrens R, Daeyaert FD, Lewi PJ, Buydens LM (1999) Using genetic algorithms for the construction of phylogenetic trees: application to G-protein coupled receptor sequences. Biosystems 49:31–43
Richard D, Olivier G (2002) Fast and accurate phylogeny reconstruction algorithm based on the minimum-evolution principle. WABI2002, LNCS2452, pp 357–374
Riley MC (2009) Significant pattern discovery in gene location and phylogeny. Ph.D. dissertation, University of Wales
Robertson B, Myers G, Howard C, Brettin T, Bukh J, Gaschen B, Gojobori T, Maertens G, Mizokami M, Nainan O, Netesov S, Nishioka K, Shin-i T, Simmonds P, Smith D, Stuyver L, Weiner A (1998) Classification, nomenclature, and database development for hepatitis C virus (HCV) and related viruses: proposals for standardization. Arch Virol 143(12):2493–2503
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425
Savolainen V, Chase MW, Hoot SB, Morton CM, Soltis DE, Bayer C, Fay MF, De Bruijn AY, Sullivan S, Qiu YL (2000) Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences. Syst Biol 49:306–362
Sedra MH, Filali HEL, Frira D (1993) Observations sur quelques caracteristiques phenotypiques et agronomiques du fruit des varieties et clones du palmier dattier selectionnes. Al Awamia 82:105–120
Sedra MH, Filali HEL, Benzine A, Allaoui M, Nour S, Boussak Z (1996) La palmeraie dattiere marocaine: evaluation du patrimonie phenicicole. Fruits 1:247–259
Sedra MH, Lashermes P, Trouslot P, Combes M, Hamon S (1998) identification and genetic diversity analysis of date palm (Phoenix dactylifera L.) varieties of Morocco using RAPD markers. Euphytica 103:75–82
Sharma DB, Karthikeyan S, Singh NP (1996) Flora of Maharashtra state, Monocotyledons. Botanical Survey of India, Calcutta, 206
Shu TLDS (2004) Freycinetia Gaudichaud. Ann Sci Nat (Paris) 3:509. 1824. In: Ke LDS, Kun S, DeFilipps RA (eds) Flora of China, vol XXIII. Science press, Beijing, pp 127–128
Soltis PS, Soltis DE (1990) Evolution of inbreeding and outcrossing in ferns and fern–allies. Plant Species Biol 5:1–11
Soltis DE, Soltis PS (1997) Phylogenetic relationships in Saxifragaceae sensu lato: a comparison of topologies based on 18 S rDNA and rbcL sequences. Am J Bot 84:504–522
Soltis DE, Soltis PS, Clegg MT, Durbin M (1990) rbcL sequence divergence and phylogenetic-relationships in Saxifragaceae sensu-lato. Proc Natl Acad Sci USA 87:4640–4644
Soltis DE, Morgan DR, Grable A, Soltis PS, Kuzoff R (1993) Molecular systematics of Saxifragaceae-sensu-stricto. Am J Bot 80:1056–1081
Soltis DE, Kuzoff RK, Conti E, Gornall R, Ferguson K (1996) matK and rbcL gene sequence data indicate that Saxifraga (Saxifragaceae) is polyphyletic. Am J Bot 83:371–382
Soltis DE, Soltis PS, Nickrent DL, Johnson LA, Hahn WJ, Hoot SB, Sweere JA, Kuzoff RK, Kron KA, Chase MW, Swensen SM, Zimmer EA, Chaw SM, Gillespie LJ, Kress WJ, Sytsma KJ (1997) Angiosperm phylogeny inferred from 18 S ribosomal DNA sequences. Ann Missouri Bot Gard 84:1–49
Soltis ED, Soltis PS (2000) Contribution of plant molecular systematics to studies of molecular evolution. Plant Mol Biol 42:45–75
Soltis DE, Kuzoff RK, Mort ME, Zanis M, Fishbein M, Hufford L, Koontz J, Arroyo MK (2001a) Elucidating deep-level phylogenetic relationships in Saxifragaceae using sequences for six chloroplastic and nuclear DNA regions. Ann Missouri Bot Gard 88:669–693
Soltis DE, Tago-Nakazawa M, Xiang QY, Kawano S, Murata J, Wakabayashi M, Hibsch-Jetter C (2001b) Phylogenetic relationships and evolution in Chrysosplenium (Saxifragaceae) based on matK sequence data. Am J Bot 88:883–893
St. John H (1972) The Indian species of Pandanus (section Rykia). Bot Mag Tokyo 85:241–262
Stone BC (1974) Towards an improved infrageneric classification in Pandanus (Pandanaceae). Bot Jahrb Syst 94:459–540
Stone BC (1976) Pandanaceae. In: Saldanha CJ, Nicolson DH (eds) Flora of Hassan district Karnataka, India. Amerind Pub. Co, Calcutta, pp 777–781
Stone BC (1981) Pandanaceae. In: Dassanayake MD, Fosberg FR (eds) A revised hand book to the flora of cylon, vol III. Oxford and IBH Pub. Co., New Delhi, pp 293–320
Studier JA, Keppler KJ (1988) A note on the neighbor-joining algorithm of Saitou and Nei. Mol Biol Evol 5:729–731
Swofford DL, Olse GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK (eds) Molecular systematics. Sinnauer Associates, Sunderland, pp 407–514
Taberlet P, Gielly L, Patou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109
Tanksley SD, Young ND, Paterson AH, Bonierbale MW (1989) RFLP mapping in plant breeding: new tools for an old science. Bio/Technology 7:257–264
Whelan S, Liò P, Goldman N (2001) Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet 17:262–272
White T, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M, Gelfand D, Sninsky J, White T (eds) PCR protocols: a guide to methods and applications. Academic, San Diego, pp 315–322
Witt CC (2004) Rates of molecular evolution and their application to neotropical avian biogeography. Ph.D. dissertation, Louisiana State University
Wolfe KH (1991) Protein coding gene in chloroplast DNA: compilation of nucleotide sequences, data base entries and rates of molecular evolution. In: Vasil K (ed) Cell culture and somatic cell genetics of plants, vol 7BI. Academic, San Diego, pp 467–482
Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substation vary greatly among plant mitochondrial, chloroplast and nuclear DNAs. Proc Natl Acad Sci USA 84:9054–9058
Wolfe KH, Sharp PM, Li WH (1989) Rates of synonymous substitution in plant nuclear genes. J Mol Evol 29:208–211
Wu X, Wan XF, Xu D, Lin GH (2005) Whole genome phylogeny based on clustered signature string composition. In: Posters in 2005 IEEE computational systems bioinformatics conference (CSB2005), Stanford University, pp 53–54
Xiaomeng W, Xiufeng W, Gang W, Dong X, Guohui L (2005) Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbor-Joining method. Int J Bioinform Res Appl 2:219–248
Yoganarasimhan SN, Subramanyam K, Razi BA (1981) Flora of Chikmagalur district, Karnataka. International Book Distributors, Dehra Dun
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Nadaf, A., Zanan, R. (2012). Phylogenetic Relationship Among the Indian Pandanus Species. In: Indian Pandanaceae - an overview. Springer, New Delhi. https://doi.org/10.1007/978-81-322-0753-5_6
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