Skip to main content
SpringerLink
Log in

Plant Taxonomy: A Historical Perspective, Current Challenges, and Perspectives

  • Protocol
  • First Online:
Molecular Plant Taxonomy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2222))

Abstract

Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science, which provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.

In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of the Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth–sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification , the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.

In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity has entered its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.

Taxonomy can justly be called the pioneering exploration of life on a little known planet.

—Wilson (2004).

The goal of discovering, describing, and classifying the species of our planet assuredly qualifies as big science.

—Wheeler et al. (2004).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 129.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Dobzhansky T (1973) Nothing in biology makes sense except in the light of evolution. Am Biol Teach 35:125–129

    Article  Google Scholar 

  2. de Carvalho MR, Bockmann FA, Amorim DS, de Vivo M, de Toledo-Piza M, Menezes NA, de Figueiredo JL, Castro RMC, Gill AC, McEachran JD, Compagno LJV, Schelly RC, Britz R, Lundberg JG, Vari RP, Nelson G (2005) Revisiting the taxonomic impediment. Science 307:353–353

    Article  PubMed  Google Scholar 

  3. Candolle AP (1813) Théorie Élémentaire de la botanique, ou Exposition des principes de la classification naturelle et de l'art de décrire et d'étudier les végétaux

    Google Scholar 

  4. Heywood VH, Watson RT (1995) Global biodiversity assessment. Cambridge University Press, Cambridge

    Google Scholar 

  5. Mayr E (1969) Principles of systematic zoology. Mcgraw-Hill, New. York

    Google Scholar 

  6. Simpson GG (1961) Principles of animal taxonomy. Columbia University Press, New York

    Book  Google Scholar 

  7. Tillier S (2000) Systématique - Ordonner la diversité du Vivant. Rapport sur la science et la technologie de l’Académie des sciences n°11. Éditions Tec & Doc

    Google Scholar 

  8. Small E (1989) Systematics of biological systematics (or taxonomy of taxonomy). Taxon 38:335–356

    Article  Google Scholar 

  9. Sprague JL, Lanjouw J, Andreas CH (1948) Minutes of the Utrecht conference. Chronica Botanica 12(1/2):12

    Google Scholar 

  10. Morton CV (1957) The misuse of the term taxon. Taxon 6(5):155

    Article  Google Scholar 

  11. Raven PH (2004) Taxonomy: where are we now? Philos Trans R Soc Lond B Biol Sci 359:729–730

    Article  PubMed  PubMed Central  Google Scholar 

  12. Pavord A (2005) The naming of names: the search for order in the world of plants. Bloomsbury, New York

    Google Scholar 

  13. Funk VA, Hoch PC, Prather LA, Wagner WL (2005) The importance of vouchers. Taxon 54:127–129

    Article  Google Scholar 

  14. Knapp S (2012) What’s in a name? A history of taxonomy. http://www.nhm.ac.uk/nature-online/science-of-natural-history/taxonomy-systematics/history-taxonomy. Accessed Jan 2012

  15. Griffing LR (2011) Who invented the dichotomous key? Richard Waller’s watercolors of the herbs of Britain. Am J Bot 98:1911–1923

    Article  PubMed  Google Scholar 

  16. Linnaeus C (1753) Species Plantarum. Stockholm

    Google Scholar 

  17. Linnaeus C (1758) Systema naturae, 10th edn. Stockholm

    Google Scholar 

  18. Candolle AP (1867) Lois de la nomenclature botanique adoptées par le Congrès international de botanique: tenu à Paris en août 1867. H. Georg, Geneva

    Google Scholar 

  19. Jussieu AL (1789) Genera plantarum. Herissant, Paris

    Google Scholar 

  20. Philippe H, Lecointre G, VanLe HL, LeGuyader H (1996) A critical study of homoplasy in molecular data with the use of a morphologically based cladogram, and its consequences for character weighting. Mol Biol Evol 13:1174–1186

    Article  Google Scholar 

  21. Lamarck J-BPAM (1809) Philosophie zoologique. Dentu, Paris

    Google Scholar 

  22. Darwin C (1859) On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. John Murray, London

    Book  Google Scholar 

  23. Haeckel E (1866) Generelle Morphologie der Organismen. Reimer, Berlin

    Book  Google Scholar 

  24. Dayrat B (2003) The roots of phylogeny: how did Haeckel build his trees? Syst Biol 52:515–527

    Article  PubMed  Google Scholar 

  25. Davis PH, Heywood PH (1963) Principles of angiosperm taxonomy. Oliver and Boyd, Edinburgh/London

    Google Scholar 

  26. Sneath PHA, Sokal RR (1963) Principles of numerical taxonomy, 7th edn. W. H. Freeman, San Francisco

    Google Scholar 

  27. Hennig W (1950) Grundzüge einer Theorie der phylogenetischen Systematik. Deutscher Zentralverlag, Berlin

    Google Scholar 

  28. Hennig W (1966) Phylogenetic systematics (tr. D. Davis and R. Zangerl), University of Illinois Press, Urbana

    Google Scholar 

  29. Godfray HCJ, Knapp S (2004) Taxonomy for the twenty-first century - introduction. Philos Trans R Soc Lond B Biol Sci 359:559–569

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Mullis K, Faloona F, Scharf S, Saiki R, Horn G, Erlich H (1986) Specific enzymatic amplification of DNA Invitro - the polymerase chain-reaction. Cold Spring Harb Symp Quant Biol 51:263–273

    Article  CAS  PubMed  Google Scholar 

  31. Bremer K, Chase MW, Stevens PF, Anderberg AA, Backlund A, Bremer B, Briggs BG, Endress PK, Fay MF, Goldblatt P, Gustafsson MHG, Hoot SB, Judd WS, Kallersjo M, Kellogg EA, Kron KA, Les DH, Morton CM, Nickrent DL, Olmstead RG, Price RA, Quinn CJ, Rodman JE, Rudall PJ, Savolainen V, Soltis DE, Soltis PS, Sytsma KJ, Thulin M, Grp AP (1998) An ordinal classification for the families of flowering plants. Ann Mo Bot Gard 85:531–553

    Article  Google Scholar 

  32. Bremer B, Bremer K, Chase MW, Reveal JL, Soltis DE, Soltis PS, Stevens PF, Anderberg AA, Fay MF, Goldblatt P, Judd WS, Kallersjo M, Karehed J, Kron KA, Lundberg J, Nickrent DL, Olmstead RG, Oxelman B, Pires JC, Rodman JE, Rudall PJ, Savolainen V, Sytsma KJ, van der Bank M, Wurdack K, Xiang JQY, Zmarzty S, Grp AP (2003) An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG II. Bot J Linn Soc 141:399–436

    Article  Google Scholar 

  33. Bremer B, Bremer K, Chase MW, Fay MF, Reveal JL, Soltis DE, Soltis PS, Stevens PF, Anderberg AA, Moore MJ, Olmstead RG, Rudall PJ, Sytsma KJ, Tank DC, Wurdack K, Xiang JQY, Zmarzty S, Grp AP (2009) An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 161:105–121

    Article  Google Scholar 

  34. The Angiosperm phylogeny group (2016) An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG IV. Bot J Linn Soc 181:1–20. https://doi.org/10.1111/boj.12385

    Article  Google Scholar 

  35. PPGI (2016) A community-derived classification for extant lycophytes and ferns. J Syst Evol 54:563–603. https://doi.org/10.1111/jse.12229

    Article  Google Scholar 

  36. Pryer KM, Schneider H, Smith AR, Cranfill R, Wolf PG, Hunt JS (2001) Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409:618–621. https://doi.org/10.1038/35054555

    Article  CAS  PubMed  Google Scholar 

  37. Bessey CE (1915) The phylogenetic taxonomy of flowering plants. Ann Mo Bot Gard 2:109–164

    Article  Google Scholar 

  38. Cronquist A (1981) An integrated system of classification of flowering plants. Columbia University Press, New York

    Google Scholar 

  39. Stebbins GL (1974) Flowering plants: evolution above the species level. Belknap press, Cambridge

    Book  Google Scholar 

  40. Takhtajan A (1997) Diversity and classification of flowering plants. Columbia University Press, New York

    Google Scholar 

  41. Thorne RF (1976) A phylogenetic classification of the Angiospermae. Evol Biol 9:35–106

    Google Scholar 

  42. Soltis DE, Soltis PS, Endress PK, Chase MW (2005) Phylogeny and evolution of angiosperms. Sinauer associates, Sunderland

    Google Scholar 

  43. Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 270:313–321

    Article  CAS  Google Scholar 

  44. May RM (2004) Tomorrow's taxonomy: collecting new species in the field will remain the rate-limiting step. Philos Trans R Soc Lond B Biol Sci 359:733–734

    Article  PubMed  PubMed Central  Google Scholar 

  45. May RM (2011) Why worry about how many species and their loss? PLoS Biol 9:e1001130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Paton AJ, Brummitt N, Govaerts R, Harman K, Hinchcliffe S, Allkin B, Lughadha EN (2008) Towards target 1 of the global strategy for plant conservation: a working list of all known plant species - progress and prospects. Taxon 57:602–611

    Google Scholar 

  47. Wilson EO (2003) The encyclopedia of life. Trends Ecol Evol 18:77–80

    Article  Google Scholar 

  48. Wilson EO (2004) Taxonomy as a fundamental discipline. Philos Trans R Soc Lond B Biol Sci 359:739–739

    Article  PubMed  PubMed Central  Google Scholar 

  49. Candolle AP (1824-1873) Prodromus systematis naturalis regni vegetabilis. Sumptibus Sociorum Treuttel et Würtz, Parisii

    Google Scholar 

  50. International Plant Names Index (2012) Published on the Internet http://www.ipni.org. Accessed July 2019

  51. Lughadha EN, Govaerts R, Belyaeva I, Black N, Lindon H, Allkin R, Magill RE, Nicolson N (2016) Counting counts: revised estimates of numbers of accepted 407 species of flowering plants, seed plants, vascular plants and land plants with a review 408 of other recent estimates. Phytotaxa 272:82–88

    Article  Google Scholar 

  52. Scotland RW, Wortley AH (2003) How many species of seed plants are there? Taxon 52:101–104

    Article  Google Scholar 

  53. The Plant List (2019) Version 1. Published on the Internet http://www.theplantlist.org/. Accessed July 2019

  54. Wortley AH, Scotland RW (2004) Synonymy, sampling and seed plant numbers. Taxon 53:478–480

    Article  Google Scholar 

  55. Mallet J, Willmott K (2003) Taxonomy: renaissance or tower of babel? Trends Ecol Evol 18:57–59

    Article  Google Scholar 

  56. Isaac NJB, Mallet J, Mace GM (2004) Taxonomic inflation: its influence on macroecology and conservation. Trends Ecol Evol 19:464–469

    Article  PubMed  Google Scholar 

  57. Meiri S, Mace GM (2007) New taxonomy and the origin of species. PLoS Biol 5:1385–1386

    Article  CAS  Google Scholar 

  58. Pillon Y, Chase MW (2007) Taxonomic exaggeration and its effects on orchid conservation. Conserv Biol 21:263–265

    Article  PubMed  Google Scholar 

  59. Crane PR (2004) Documenting plant diversity: unfinished business. Philos Trans R Soc Lond B Biol Sci 359:735–737

    Article  PubMed  PubMed Central  Google Scholar 

  60. Joppa LN, Roberts DL, Pimm SL (2011) How many species of flowering plants are there? Proc R Soc B Biol Sci 278:554–559

    Article  Google Scholar 

  61. Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B (2011) How many species are there on earth and in the ocean? PLoS Biol 9:e1001127

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Bisby FA, Roskov YR, Orrell TM, Nicolson D, Paglinawan LE et al (2010) Species 2000 & ITIS Catalogue of Life: 2010 Annual Checklist. Digital resource at http://www.catalogueoflife.org/annual-checklist/2010. Species 2000, Reading, UK

  63. Caldecott JO, Jenkins MD, Johnson TH, Groombridge B (1996) Priorities for conserving global species richness and endemism. Biodivers Conserv 5:699–727

    Article  Google Scholar 

  64. Joppa LN, Roberts DL, Myers N, Pimm SL (2011) Biodiversity hotspots house most undiscovered plant species. Proc Natl Acad Sci U S A 108:13171–13176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Callmander MW, Schatz GE, Lowry PP (2005) IUCN red list assessment and the global strategy for plant conservation: taxonomists must act now. Taxon 54:1047–1050

    Article  Google Scholar 

  66. Godfray HCJ (2002) Challenges for taxonomy - the discipline will have to reinvent itself if it is to survive and flourish. Nature 417:17–19

    Article  CAS  PubMed  Google Scholar 

  67. Funk VA (2006) Floras: a model for biodiversity studies or a thing of the past? Taxon 55:581–588

    Article  Google Scholar 

  68. Wheeler QD, Raven PH, Wilson EO (2004) Taxonomy: impediment or expedient? Science 303:285–285

    Article  CAS  PubMed  Google Scholar 

  69. Wheeler QD, Knapp S et al (2012) Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity. Syst Biodivers 10(1):1–20

    Article  CAS  Google Scholar 

  70. Ebach MC, Valdecasas AG, Wheeler QD (2011) Impediments to taxonomy and users of taxonomy: accessibility and impact evaluation. Cladistics 27:550–557

    Article  PubMed  Google Scholar 

  71. Ronquist F, Gardenfors U (2003) Taxonomy and biodiversity inventories: time to deliver. Trends Ecol Evol 18:269–270

    Article  Google Scholar 

  72. Joly CA (2006) Taxonomy: programmes developing in the south too. Nature 440:24–24

    Article  CAS  PubMed  Google Scholar 

  73. Schatz GE, Lowry PP, Ramisamihantanirina A (1998) Takhtajania perrieri rediscovered. Nature 391:133–134

    Article  CAS  Google Scholar 

  74. Jones WG, Hill KD, Allen JM (1995) Wollemia nobilis, a new living Australian genus and species in the Araucariaceae. Telopea 6:173–176

    Article  Google Scholar 

  75. Mabberley DJ (2009) Exploring Terra Incognita. Science 324:472–472

    Article  CAS  PubMed  Google Scholar 

  76. Thulin M (2007) Acacia fumosa sp nov (Fabaceae) from eastern Ethiopia. Nord J Bot 25:272–274

    Article  Google Scholar 

  77. Dransfield J, Rakotoarinivo M, Baker WJ, Bayton RP, Fisher JB, Horn JW, Leroy B, Metz X (2008) A new coryphoid palm genus from Madagascar. Bot J Linn Soc 156:79–91

    Article  Google Scholar 

  78. Agnarsson I, Kuntner M (2007) Taxonomy in a changing world: seeking solutions for a science in crisis. Syst Biol 56:531–539

    Article  PubMed  Google Scholar 

  79. Crisci JV (2006) One-dimensional systematist: perils in a time of steady progress. Syst Bot 31:217–221

    Article  Google Scholar 

  80. Joppa LN, Roberts DL, Pimm SL (2011) The population ecology and social behaviour of taxonomists. Trends Ecol Evol 26:551–553

    Article  PubMed  Google Scholar 

  81. Rodman JE, Cody JH (2003) The taxonomic impediment overcome: NSF's partnerships for enhancing expertise in taxonomy (PEET) as a model. Syst Biol 52:428–435

    Article  PubMed  Google Scholar 

  82. Bebber DP et al (2012) Big hitting collectors make massive and disproportionate contribution to the discovery of plant species. Proc R Soc Lond B Biol Sci 279(1736):2269–2274

    Google Scholar 

  83. Thiers B (2019) Index herbarium: a global directory of public herbaria and associated staff. New York Botanical Garden’s Virtual Herbarium. http://sweetgum.nybg.org/ih/

  84. Bebber DP, Carine MA, Wood JRI, Wortley AH, Harris DJ, Prance GT, Davidse G, Paige J, Pennington TD, Robson NKB, Scotland RW (2010) Herbaria are a major frontier for species discovery. Proc Natl Acad Sci U S A 107:22169–22171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Fontaine B, Perrard A, Bouchet P (2012) 21 years of shelf life between discovery and description of new species. Curr Biol 22(22):R943–R944. https://doi.org/10.1016/j.cub.2012.10.029

    Article  CAS  PubMed  Google Scholar 

  86. Le Bras G, Pignal M, Jeanson ML, Muller S, Aupic C, Carré B, Flament G, Gaudeul M, Gonçalves C, Invernón VR, Jabbour F, Lerat E, Lowry PP, Offroy B, Pérez Pimparé E, Poncy O, Rouhan G, Haevermans T (2017) The French Muséum national d’histoire naturelle vascular plant herbarium collection dataset. Scientific Data 4:170016

    Article  PubMed  PubMed Central  Google Scholar 

  87. Godfray HCJ, Clark BR, Kitching IJ, Mayo SJ, Scoble MJ (2007) The web and the structure of taxonomy. Syst Biol 56:943–955

    Article  CAS  PubMed  Google Scholar 

  88. Knapp S, McNeill J, Turland NJ (2011) Changes to publication requirements made at the XVIII International Botanical Congress in Melbourne - what does e-publication mean for you? PhytoKeys (6):5–11

    Google Scholar 

  89. Nicolson N, Challis K, Tucker A, Knapp S (2017) Impact of e-publication changes in the International Code of Nomenclature for algae, fungi and plants (Melbourne Code, 2012) - did we need to “run for our lives”? BMC Evol Biol 17:116. https://doi.org/10.1186/s12862-017-0961

    Article  PubMed  PubMed Central  Google Scholar 

  90. Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Syst Biol 54:852–859

    Article  PubMed  Google Scholar 

  91. Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R (2005) Towards writing the encyclopaedia of life: an introduction to DNA barcoding. Philos Trans R Soc B Biol Sci 360:1805–1811

    Article  CAS  Google Scholar 

  92. Wiens JJ (2007) Species delimitation: new approaches for discovering diversity. Syst Biol 56:875–878

    Article  PubMed  Google Scholar 

  93. Pannell JR (2009) Mating-system evolution: succeeding by celibacy. Curr Biol 19:R983–R985

    Article  CAS  PubMed  Google Scholar 

  94. Hood ME, Antonovics J (2003) Plant species descriptions show signs of disease. Proc R Soc Lond B Biol Sci 270:S156–S158

    Article  Google Scholar 

  95. Duminil J, Di Michele M (2009) Plant species delimitation: a comparison of morphological and molecular markers. Plant Biosystems 143:528–542

    Article  Google Scholar 

  96. Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, Winker K, Ingram KK, Das I (2007) Cryptic species as a window on diversity and conservation. Trends Ecol Evol 22:148–155

    Article  PubMed  Google Scholar 

  97. Grundt HH, Kjolner S, Borgen L, Rieseberg LH, Brochmann C (2006) High biological species diversity in the arctic flora. Proc Natl Acad Sci U S A 103:972–975

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Pillon Y, Hopkins HCF, Munzinger J, Amir H, Chase MW (2009) Cryptic species, gene recombination and hybridization in the genus Spiraeanthemum (Cunoniaceae) from New Caledonia. Bot J Linn Soc 161:137–152

    Article  Google Scholar 

  99. Dulvy NK, Reynolds JD (2009) BIODIVERSITY skates on thin ice. Nature 462:417–417

    Article  CAS  PubMed  Google Scholar 

  100. Robertson A, Newton AC, Ennos RA (2004) Multiple hybrid origins, genetic diversity and population genetic structure of two endemic Sorbus taxa on the Isle of Arran, Scotland. Mol Ecol 13:123–134

    Article  CAS  PubMed  Google Scholar 

  101. Squirrell J, Hollingsworth PM, Bateman RM, Tebbitt MC, Hollingsworth ML (2002) Taxonomic complexity and breeding system transitions: conservation genetics of the Epipactis leptochila complex (Orchidaceae). Mol Ecol 11:1957–1964

    Article  CAS  PubMed  Google Scholar 

  102. van Dijk PJ (2003) Ecological and evolutionary opportunities of apomixis: insights from Taraxacum and Chondrilla. Philos Trans R Soc Lond Ser B Biol Sci 358:1113–1121

    Article  CAS  Google Scholar 

  103. Ennos RA, French GC, Hollingsworth PM (2005) Conserving taxonomic complexity. Trends Ecol Evol 20:164–168

    Article  PubMed  Google Scholar 

  104. Ennos RA, Whitlock R, Fay MF, Jones B, Neaves LE, Payne R, Taylor I, De Vere N, Hollingsworth PM (2012) Process-based species action plans: an approach to conserve contemporary evolutionary processes that sustain diversity in taxonomically complex groups. Bot J Linn Soc 168:194–203

    Article  Google Scholar 

  105. Li FW, Tan BC, Buchbender V, Moran RC, Rouhan G, Wang CN, Quandt D (2009) Identifying a mysterious aquatic fern gametophyte. Plant Syst Evol 281:77–86

    Article  Google Scholar 

  106. Van Deynze A, Stoffel K (2006) High-throughput DNA extraction from seeds. Seed Sci Technol 34:741–745

    Article  Google Scholar 

  107. Asif MJ, Cannon CH (2005) DNA extraction from processed wood: a case study for the identification of an endangered timber species (Gonystylus bancanus). Plant Mol Biol Report 23:185–192

    Article  CAS  Google Scholar 

  108. Colpaert N, Cavers S, Bandou E, Caron H, Gheysen G, Lowe AJ (2005) Sampling tissue for DNA analysis of trees: trunk cambium as an alternative to canopy leaves. Silvae Genetica 54:265–269

    Article  Google Scholar 

  109. Rachmayanti Y, Leinemann L, Gailing O, Finkeldey R (2006) Extraction, amplification and characterization of wood DNA from Dipterocarpaceae. Plant Mol Biol Report 24:45–55

    Article  CAS  Google Scholar 

  110. Tibbits JFG, McManus LJ, Spokevicius AV, Bossinger G (2006) A rapid method for tissue collection and high-throughput isolation of genomic DNA from mature trees. Plant Mol Biol Report 24:81–91

    Article  CAS  Google Scholar 

  111. Novaes RML, Rodrigues JG, Lovato MB (2009) An efficient protocol for tissue sampling and DNA isolation from the stem bark of Leguminosae trees. Genet Mol Res 8:86–96

    Article  CAS  PubMed  Google Scholar 

  112. Deguilloux MF, Pemonge MH, Petit RJ (2002) Novel perspectives in wood certification and forensics: dry wood as a source of DNA. Proc R Soc B Biol Sci 269:1039–1046

    Article  CAS  Google Scholar 

  113. Hiiesalu I, Opik M, Metsis M, Lilje L, Davison J, Vasar M, Moora M, Zobel M, Wilson SD, Partel M (2012) Plant species richness belowground: higher richness and new patterns revealed by next-generation sequencing. Mol Ecol 21:2004–2016

    Article  CAS  PubMed  Google Scholar 

  114. Kesanakurti PR, Fazekas AJ, Burgess KS, Percy DM, Newmaster SG, Graham SW, Barrett SCH, Hajibabaei M, Husband BC (2011) Spatial patterns of plant diversity below-ground as revealed by DNA barcoding. Mol Ecol 20:1289–1302

    Article  PubMed  Google Scholar 

  115. Dunn CP (2003) Keeping taxonomy based in morphology. Trends Ecol Evol 18:270–271

    Article  Google Scholar 

  116. Santos LM, Faria LRR (2011) The taxonomy’s new clothes: a little more about the DNA-based taxonomy. Zootaxa 3025:66–68

    Article  Google Scholar 

  117. Schaefer H, Carine MA, Rumsey FJ (2011) From European priority species to invasive weed: Marsilea azorica (Marsileaceae) is a misidentified alien. Syst Bot 36:845–853

    Article  Google Scholar 

  118. Launert GOE, Paiva JAR (1983) Iconographia selecta florae Azoricae. Coimbra 2:159

    Google Scholar 

  119. Lipscomb D, Platnick N, Wheeler Q (2003) The intellectual content of taxonomy: a comment on DNA taxonomy. Trends Ecol Evol 18:65–66

    Article  Google Scholar 

  120. Sites JW, Marshall JC (2004) Operational criteria for delimiting species. Annu Rev Ecol Evol Syst 35:199–227

    Article  Google Scholar 

  121. Stace CA (2005) Plant taxonomy and biosystematics - does DNA provide all the answers? Taxon 54:999–1007

    Article  Google Scholar 

  122. Linder CR, Rieseberg LH (2004) Reconstructing patterns of reticulate evolution UN plants. Am J Bot 91:1700–1708

    Article  PubMed  PubMed Central  Google Scholar 

  123. Vriesendorp B, Bakker FT (2005) Reconstructing patterns of reticulate evolution in angiosperms: what can we do? Taxon 54:593–604

    Article  Google Scholar 

  124. Egan AN, Schlueter J, Spooner DM (2012) Applications of next-generation sequencing in plant biology. Am J Bot 99:175–185

    Article  CAS  PubMed  Google Scholar 

  125. Harrison N, Kidner CA (2011) Next-generation sequencing and systematics: what can a billion base pairs of DNA sequence data do for you? Taxon 60:1552–1566

    Article  Google Scholar 

  126. Straub SCK, Parks M, Weitemier K, Fishbein M, Cronn RC, Liston A (2012) Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics. Am J Bot 99:349–364

    Article  CAS  PubMed  Google Scholar 

  127. Bakker FT (2015) DNA sequences from plant herbarium tissue (Chapter 8). In: Hörandl E, Appelhans MS (eds) Next-generation sequencing in plant systematics. International Association for Plant Taxonomy (IAPT). https://doi.org/10.14630/000009

  128. Richardson JE, Pennington RT, Pennington TD, Hollingsworth PM (2001) Rapid diversification of a species-rich genus of neotropical rain forest trees. Science 293:2242–2245

    Article  CAS  PubMed  Google Scholar 

  129. Baldwin BG, Sanderson MJ (1998) Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proc Natl Acad Sci U S A 95:9402–9406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Wang AL, Yang MH, Liu JQ (2005) Molecular phylogeny, recent radiation and evolution of gross morphology of the rhubarb genus Rheum (Polygonaceae) inferred from chloroplast DNA trnL-F sequences. Ann Bot 96:489–498

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Hodges SA, Arnold ML (1994) Columbines - a geographically widespread species flock. Proc Natl Acad Sci U S A 91:5129–5132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Linder HP (2008) Plant species radiations: where, when, why? Philos Trans R Soc B Biol Sci 363:3097–3105

    Article  Google Scholar 

  133. Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP (2003) A plea for DNA taxonomy. Trends Ecol Evol 18:70–74

    Article  Google Scholar 

  134. Hey J, Pinho C (2012) Population genetics and objectivity in species diagnosis. Evolution 66:1413–1429

    Article  PubMed  PubMed Central  Google Scholar 

  135. Knowles L, Carstens B (2007) Delimiting species without monophyletic gene trees. Syst Biol 56:887–895

    Article  PubMed  Google Scholar 

  136. Staats M, Cuenca A, Richardson JE, Vrielink-van Ginkel R, Petersen G, Seberg O, Bakker FT (2011) DNA damage in plant herbarium tissue. PLoS One 6:e28448

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Seberg O, Humphries CJ, Knapp S, Stevenson DW, Petersen G, Scharff N, Andersen NM (2003) Shortcuts in systematics? A commentary on DNA-based taxonomy. Trends Ecol Evol 18:63–65

    Article  Google Scholar 

  138. Lister DL, Bower MA, Howe CJ, Jones MK (2008) Extraction and amplification of nuclear DNA from herbarium specimens of emmer wheat: a method for assessing DNA preservation by maximum amplicon length recovery. Taxon 57:254–258

    Google Scholar 

  139. Wandeler P, Hoeck PEA, Keller LF (2007) Back to the future: museum specimens in population genetics. Trends Ecol Evol 22:634–642

    Article  PubMed  Google Scholar 

  140. Cozzolino S, Cafasso D, Pellegrino G, Musacchio A, Widmer A (2007) Genetic variation in time and space: the use of herbarium specimens to reconstruct patterns of genetic variation in the endangered orchid Anacamptis palustris. Conserv Genet 8:629–639

    Article  Google Scholar 

  141. Erkens RHJ, Cross H, Maas JW, Hoenselaar K, Chatrou LW (2008) Assessment of age and greenness of herbarium specimens as predictors for successful extraction and amplification of DNA. Blumea 53:407–428

    Article  Google Scholar 

  142. Drabkova L, Kirschner J, Vlcek C (2002) Comparison of seven DNA extraction and amplification protocols in historical herbarium specimens of Juncaceae. Plant Mol Biol Report 20:161–175

    Article  CAS  Google Scholar 

  143. Jankowiak K, Buczkowska K, Szweykowska-Kulinska Z (2005) Successful extraction of DNA from 100-year-old herbarium specimens of the liverwort Bazzania trilobata. Taxon 54:335–336

    Article  Google Scholar 

  144. Korpelainen H, Pietilainen M (2008) Effort to reconstruct past population history in the fern Blechnum spicant. J Plant Res 121:293–298

    Article  PubMed  Google Scholar 

  145. Savolainen V, Cuenoud P, Spichiger R, Martinez MDP, Crevecoeur M, Manen JF (1995) The use of herbarium specimens in DNA Phylogenetics - evaluation and improvement. Plant Syst Evol 197:87–98

    Article  CAS  Google Scholar 

  146. Ribeiro RA, Lovato MB (2007) Comparative analysis of different DNA extraction protocols in fresh and herbarium specimens of the genus Dalbergia. Genet Mol Res 6:173–187

    CAS  PubMed  Google Scholar 

  147. Andreasen K, Manktelow M, Razafimandimbison SG (2009) Successful DNA amplification of a more than 200-year-old herbarium specimen: recovering genetic material from the Linnaean era. Taxon 58:959–962

    Article  Google Scholar 

  148. Ames M, Spooner DM (2008) DNA from herbarium specimens settles a controversy about origins of the European potato. Am J Bot 95:252–257

    Article  CAS  PubMed  Google Scholar 

  149. Walters C, Reilley AA, Reeves PA, Baszczak J, Richards CM (2006) The utility of aged seeds in DNA banks. Seed Sci Res 16:169–178

    Article  CAS  Google Scholar 

  150. Alves RJV, Machado MD (2007) Is classical taxonomy obsolete? Taxon 56:287–288

    Article  Google Scholar 

  151. DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc B Biol Sci 360:1905–1916

    Article  CAS  Google Scholar 

  152. DeSalle R (2006) Species discovery versus species identification in DNA barcoding efforts: response to Rubinoff. Conserv Biol 20:1545–1547

    Article  PubMed  Google Scholar 

  153. Schlick-Steiner BC, Steiner FM, Seifert B, Stauffer C, Christian E, Crozier RH (2010) Integrative taxonomy: a multisource approach to exploring biodiversity. Annu Rev Entomol 55:421–438

    Article  CAS  PubMed  Google Scholar 

  154. Dayrat B (2005) Towards integrative taxonomy. Biol J Linn Soc 85:407–415

    Article  Google Scholar 

  155. Wheeler QD (2005) Losing the plot: DNA “barcodes” and taxonomy. Cladistics 21:405–407

    Article  PubMed  Google Scholar 

  156. Corney DPA, Clark JY, Tang HT, Wilkin P (2012) Automatic extraction of leaf characters from herbarium specimens. Taxon 61(1):231–244

    Article  Google Scholar 

  157. Raxworthy CJ, Ingram CM, Rabibisoa N, Pearson RG (2007) Applications of ecological niche modeling for species delimitation: a review and empirical evaluation using day geckos (Phelsuma) from Madagascar. Syst Biol 56:907–923

    Article  PubMed  Google Scholar 

  158. Rissler LJ, Apodaca JJ (2007) Adding more ecology into species delimitation: ecological niche models and phylogeography help define cryptic species in the black salamander (Aneides flavipunctatus). Syst Biol 56:924–942

    Article  PubMed  Google Scholar 

  159. Wiens JJ, Graham CH (2005) Niche conservatism: integrating evolution, ecology, and conservation biology. Annu Rev Ecol Evol Syst 36:519–539

    Article  Google Scholar 

  160. Brautigam A, Gowik U (2010) What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biol 12:831–841

    Article  CAS  PubMed  Google Scholar 

  161. Cronn R, Knaus BJ, Liston A, Maughan PJ, Parks M, Syring JV, Udall J (2012) Targeted enrichment strategies for next-generation plant biology. Am J Bot 99:291–311

    Article  CAS  PubMed  Google Scholar 

  162. Rodriguez-Fernandez JI, De Carvalho CJB, Pasquini C, De Lima KMG, Moura MO, Arizaga GGC (2011) Barcoding without DNA? Species identification using near infrared spectroscopy. Zootaxa 46–54

    Google Scholar 

  163. Munck L, Jespersen BM, Rinnan A, Seefeldt HF, Engelsen MM, Norgaard L, Engelsen SB (2010) A physiochemical theory on the applicability of soft mathematical models-experimentally interpreted. J Chemom 24:481–495

    Article  CAS  Google Scholar 

  164. Cruickshank RH, Munck L (2011) It’s barcoding Jim, but not as we know it. Zootaxa 2933:55–56

    Article  Google Scholar 

  165. Andres-Sanchez S, Rico E, Herrero A, Santos-Vicente M, Martinez-Ortega MM (2009) Combining traditional morphometrics and molecular markers in cryptic taxa: towards an updated integrative taxonomic treatment for Veronica subgenus Pentasepalae (Plantaginaceae sensu APG II) in the western Mediterranean. Bot J Linn Soc 159:68–87

    Article  Google Scholar 

  166. Schlick-Steiner BC, Seifert B, Stauffer C, Christian E, Crozier RH, Steiner FM (2007) Without morphology, cryptic species stay in taxonomic crypsis following discovery. Trends Ecol Evol 22:391–392

    Article  PubMed  Google Scholar 

  167. Blaxter M, Mann J, Chapman T, Thomas F, Whitton C, Floyd R, Abebe E (2005) Defining operational taxonomic units using DNA barcode data. Philos Trans R Soc B Biol Sci 360:1935–1943

    Article  CAS  Google Scholar 

  168. Markmann M, Tautz D (2005) Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Philos Trans R Soc B Biol Sci 360:1917–1924

    Article  CAS  Google Scholar 

  169. Pleijel F, Jondelius U, Norlinder E, Nygren A, Oxelman B, Schander C, Sundberg P, Thollesson M (2008) Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. Mol Phylogenet Evol 48:369–371

    Article  CAS  PubMed  Google Scholar 

  170. Puillandre N, Bouchet P, Boisselier-Dubayle MC, Brisset J, Buge B, Castelin M, Chagnoux S, Christophe T, Corbari L, Lambourdiere J, Lozouet P, Marani G, Rivasseau A, Silva N, Terryn Y, Tillier S, Utge J, Samadi S (2012) New taxonomy and old collections: integrating DNA barcoding into the collection curation process. Mol Ecol Resour 12:396–402

    Article  CAS  PubMed  Google Scholar 

  171. Gemeinholzer B, Bachmann K (2005) Examining morphological and molecular diagnostic character states of Cichorium intybus L. (Asteraceae) and C-spinosum L. Plant Syst Evol 253:105–123

    Article  CAS  Google Scholar 

  172. Bacon CD, McKenna MJ, Simmons MP, Wagner WL (2012) Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia). BMC Evol Biol 12:23

    Article  PubMed  PubMed Central  Google Scholar 

  173. Barrett CF, Freudenstein JV (2011) An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid. Mol Ecol 20:2771–2786

    Article  PubMed  Google Scholar 

  174. Koffi KG, Heuertz M, Doumenge C, Onana JM, Gavory F, Hardy OJ (2010) A combined analysis of morphological traits, chloroplast and nuclear DNA sequences within Santiria trimera (Burseraceae) suggests several species following the biological species concept. Plant Ecol Evol 143:160–169

    Article  Google Scholar 

  175. Ley AC, Hardy OJ (2010) Species delimitation in the central African herbs Haumania (Marantaceae) using georeferenced nuclear and chloroplastic DNA sequences. Mol Phylogenet Evol 57:859–867

    Article  CAS  PubMed  Google Scholar 

  176. Meudt HM, Lockhart PJ, Bryant D (2009) Species delimitation and phylogeny of a New Zealand plant species radiation. BMC Evol Biol 9:111

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  177. Schmidt-Lebuhn AN (2007) Using amplified fragment length polymorphism (AFLP) to unravel species relationships and delimitations in Minthostachys (Labiatae). Bot J Linn Soc 153:9–19

    Article  Google Scholar 

  178. Zeng YF, Liao WJ, Petit RJ, Zhang DY (2010) Exploring species limits in two closely related Chinese oaks. PLoS One 5:e15529

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  179. Rieseberg LH, Troy TE, Baack EJ (2006) The nature of plant species. Nature 440:524–527

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  180. de Queiroz K (2005) Ernst Mayr and the modern concept of species. Proc Natl Acad Sci U S A 102:6600–6607

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  181. de Queiroz K (2007) Species concepts and species delimitation. Syst Biol 56(6):879–886

    Article  PubMed  Google Scholar 

  182. Wright S (1940) The statistical consequences of Mendelian heredity in relation to speciation. In: Huxley J (ed) The new systematics. Oxford university press, London, pp 161–183

    Google Scholar 

  183. Mayr E (1942) Systematics and the origin of species. Columbia university press, New York

    Google Scholar 

  184. Dobzhansky T (1950) Mendelian populations and their evolution. Am Nat 84:401–418

    Article  Google Scholar 

  185. Poulton EB (1904) What is a species? Proc Entomol Soc Lond 1903:lxxviicxvi

    Google Scholar 

  186. Dobzhansky T (1970) Genetics of the evolutionary process. Columbia University Press, New York

    Google Scholar 

  187. Sokal RR, Crovello TJ (1970) The biological species concept: a critical evaluation. Am Nat 104:107–123

    Article  Google Scholar 

  188. Van Valen L (1976) Ecological species, multispecies, and oaks. Taxon 25:233–239

    Article  Google Scholar 

  189. Simpson GG (1951) The species concept. Evolution 5:285–298

    Article  Google Scholar 

  190. Wiley EO (1978) The evolutionary species concept reconsidered. Syst Zool 21:17–26

    Article  Google Scholar 

  191. Cracraft J (1989) Speciation and its ontology: the empirical consequences of alternative species concepts for understanding patterns and processes of differentiation. In: Otte D, Endler JA (eds) Speciation and its consequences. Sinauer Associates, Sunderland, pp 28–59

    Google Scholar 

  192. Rosen DE (1979) Fishes from the uplands and intermontane basins of Guatemala: revisionary studies and comparative geography. Bull Am Mus Nat Hist 162:267–376

    Google Scholar 

  193. Donoghue MJ (1985) A critique of the biological species concept and recommendations for a phylogenetic alternative. Bryologist 88:172–181

    Article  Google Scholar 

  194. Mishler BD (1985) The morphological, developmental, and phylogenetic basis of species concepts in bryophytes. Bryologist 88:207–214

    Article  Google Scholar 

  195. Baum DA, Shaw KL (1995) Genealogical perspectives on the species problem. In: Hoch PC, Stephenson AG (eds) Experimental and molecular approaches to plant biosystematics. Missouri Botanical Garden, St. Louis, pp 289–303

    Google Scholar 

  196. Mallet J (1995) A species definition for the modern synthesis. Trends Ecol Evol 10:294–299

    Article  CAS  PubMed  Google Scholar 

  197. Templeton AR (1998) Species and speciation: geography, population structure, ecology, and gene trees. In: Howard DJ, Berlocher SH (eds) Endless forms: species and speciation. Oxford university press, New York, pp 32–43

    Google Scholar 

  198. Sites JW, Marshall JC (2003) Delimiting species: a renaissance issue in systematic biology. Trends Ecol Evol 18(9):462–470

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France

    Germinal Rouhan & Myriam Gaudeul

Authors
  1. Germinal Rouhan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Myriam Gaudeul
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Germinal Rouhan .

Editor information

Editors and Affiliations

  1. UMR PVBMT, Universite de la Reunion, St Pierre, Réunion, France

    Pascale Besse

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Rouhan, G., Gaudeul, M. (2021). Plant Taxonomy: A Historical Perspective, Current Challenges, and Perspectives. In: Besse, P. (eds) Molecular Plant Taxonomy. Methods in Molecular Biology, vol 2222. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0997-2_1

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-0997-2_1

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0996-5

  • Online ISBN: 978-1-0716-0997-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation