Indian Journal of Science and Technology

Open Access Open Access  Restricted Access Subscription Access

Ethnobotany Genomics - Use of DNA Barcoding to Explore Cryptic Diversity in Economically Important Plants


Affiliations
1 Biodiversity Institute of Ontario Herbarium, University of Guelph, Guelph, Ontario, Canada. N1G 2W1, Canada
 

The ethnobotany genomics concept is founded on the idea of 'assemblage' of biodiversity knowledge. This includes a coming together of different ways of knowing and valorizing species variation in a novel approach seeking to add value to both traditional knowledge (TK) and scientific knowledge (SK). Ethnobotany genomics is defined as exploring the variation in genomic sequences from many species, and here we present some of our recent work that demonstrates the potential benefits of this approach for ethnobotanical research with economic implications. DNA barcoding was used to identify Acacia and nutmeg taxa that are economically important to society-at-large. Furthermore we identified considerable variation that is recognized by several indigenous cultures. The impacts of ethnobotany genomics will extend well beyond biodiversity science. Explorations of the genomic properties across the expanse of life are now possible using DNA barcoding to assemble sequence information for a standard portion of the genome from large assemblages of species. Perhaps the most important contribution is major barcode projects will leave an important legacy; a comprehensive repository of highquality DNA extracts that will facilitate future genomic investigations.

Keywords

DNA Barcoding, Economic Botany, Biodiversity, Plant Diversity, Ethnopharmacology,Ethnomedicine, Ethnobiology, Biotechnology
User

  • Bentham G (1840) Contributions towards a flora of South America — enumeration of plants collected by Mr. Schomburgk in British Guiana. J. Botany (Hooker). 2, 127–146.

  • Bentham G (1842) Notes on Mimoseae, with a short synopsis of species. Journal of Botany (Hooker). 4, 323–418.

  • Blaxter ML (2004) The promise of a DNA taxonomy. Phil.l Trans. Royal Soc. London Series B. Biol. Sci. 359, 669–679.

  • Blaxter ML and Floyd R (2003) Molecular taxonomics for biodiversity surveys: already a reality. Trends in Ecol. Evol. 18, 268–269.

  • Brenan JPM (1983) Manual on Taxonomy of Acacia Species: Present Taxonomy of Four Species of Acacia (A. albida, A. senegal, A. nilotica and A. tortilis), pp. 20– 35. FAO, Rome, Italy.

  • Byrne M, Tischler G, Macdonald B, Coates DJ and McComb J (2001) Phylogenetic relationships between two rare acacias and their common, widespread relatives in south-western Australia. Conservation Genetics. 2, 157–166.

  • Chase MW, Salamin N, Wilkinson M et al. (2005) Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Soc. B: Biol.Sci. 360, 1889–1895.

  • Cowan RS, Chase MW, Kress WJ and Savolainen V (2006) 300 000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon. 55, 611–616.

  • Erickson DL, Spouge J, Resch A, Weigt LE and Kress WJ (2008) DNA barcoding in land plants: developing standards to quantify and maximize success. Taxon. 57, 1304–1316.

  • Fagg CW and Greaves A (1990) Acacia Nilotica 1869– 1988, Annotated Bibliography No. F42 (ed. Langdon K), CAB International, published in collaboration with the Oxford Forestry Institute, Wallingford, UK.

  • Fazekas AJ, Burgess KS, Kesanakurti PR, Percy DM, Hajibabaei M, Graham SW, Husband BC, Barrett SCH and Newmaster SG (2008) Assessing the utility of coding and non-coding genomic regions for plant DNA barcoding. PLOS ONE. 3, 1-12.

  • Fazekas AJ, Kesanakurti PR, Burgess KS, Percy DM, Graham SW, Barrett SCH, Newmaster SG, Hajibabaei M and Husband BC (2009) Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Mol. Ecol. Resources. 9, 130–139.

  • Funk DJ and Omland KE (2003) Species-level paraphyly and polyphyly: frequency, causes and consequences, with insights from animal mitochondrial DNA. Ann. Rev. Ecol., Evol. Systematics. 34, 397–423.

  • Gaston KJ and O’Neill MA (2004) Automated species identification: Why not? Phil. Trans. Royal Soc. London Series B. 359, 340–387.

  • Godfray HCJ (2002a) Challenges for taxonomy. Nature. 417, 17–19.

  • Godfray HCJ (2002b) Towards taxonomy’s ‘glorious revolution’. Nature. 420, 461.

  • Godfray HCJ and Knapp S (2004) Introduction. in taxonomy for the twenty-first century–special issue. Phil. Trans. Royal Soc. London Series B. 359, 559–569.

  • Grant B (2009) A Fading Field Traditional taxonomists are an endangered species. Could their unique brand of knowledge disappear, too? Scientist. 23(6), 32-33.

  • Hammond, P. (1992) ‘Species inventory’, in Groombridge, B. (Ed.): Global Biodiversity: Status of the Earth’s Living Resources, pp.17–39. Chapman and Hall, London,

  • Hawksworth DL and Kalin-Arroyo MT (1995) Magnitude and distribution of biodiversity in Heywood, V.H. (Ed.). In Global biodiversity Assessment, pp.107–191. Cambridge University Press, UK.

  • Hebert PDN and Gregory TR (2005) The Promise of DNA barcoding for taxonomy. Sys. Biol. 54(5), 852–859.

  • Hebert PDN, Cywinska A, Ball SL and DeWaard JR (2003) Biological identification through DNA barcodes. Proc. Royal Soc. B: Biol. Sci. 270, 313–321.

  • Heinrich M (2000) Ethnobotany and its role in drug development. Phytotherapy Research 14, 479–488.

  • Jain SK and Rao RR (1977) A Handbook of field and Herbarium Methods. Today and Tomorrow’s Printers & Publishers, New Delhi.

  • Janovec JP and Harrison JS (2002) A morphological analysis of the Compsoneura sprucei complex (Myristicaceae), with a new combination for the Central American species Compsoneura mexicana. Sys. Bot. 27, 662-673.

  • Janovec JP and Neill AK (2002) Studies of the Myristicaceae: an overview of the Compsoneura atopa complex, with descriptions of new species from Columbia. Brittonia. 54, 251–261.

  • Kress J and Erickson DL (2008) DNA barcodes: genes, genomics, and bioinformatics. Proc. Natl. Acad. Sci., USA. 105, 2761–2762.

  • Kress WJ and Erickson DL (2007) A two-locus global DNA barcode for land plants: the coding rbcl gene complements the non-coding trnH-psbA spacer region. Public Library of Science ONE. 2, e508. doi: 10.1371/journal.pone.0000508.

  • Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences, USA, 102, 8369–8374.

  • Kriticos DJ, Sutherst RW, Brown JR, Adkins SW and Maywald GF (2003) Climate change and the potential distribution of an invasive alien plant: Acacia nilotica ssp. indica in Australia. J. Appl. Ecol. 40, 111–124.

  • Lahaye R, van der Bank M, Bogarin D et al. (2008) DNA barcoding the floras of biodiversity hotspots. Proc. Natl. Acad. Sci., USA. 105, 2923–2928. doi: 10.1073/ pnas.0709936105.

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

  • Luckow M, Miller JT, Murphy DJ, Livshultz T (2003) A phylogenetic analysis of the Mimosoideae (Leguminosae) based on chloroplast DNA sequence data. In: Advances in Legume Systematics, Part 10, Higher Level Systematics (eds. Klitgaard BB & Bruneau A), pp. 197–220. Royal Botanical Gardens, Kew, UK.

  • Macedo DS and Anderson AB (1993) Early Ecological Changes Associated with Logging in an Amazon Floodplain. Biotropica. 25(2), 151-163.

  • Maslin BR, Miller JT and Seiger DS (2003) Overview of the generic status of Acacia (Leguminosae: Mimosoideae). Aus. Sys. Bot. 16, 1–18.

  • May RM (1988) How many species are there on Earth? Science. 241, 1441–1449.

  • McDonald MW, Maslin BR and Butcher PA (2001) Utilisation of acacias. In: Flora of Australia, Volume 11A, Mimosaceae, Acacia Part 1 (eds. Orchard AE, Wilson AJG), pp. 30–40. ABRS/CSIRO Publishing, Melbourne, Australia.

  • Midgley SJ and Turnbull JW (2003) Domestication and use of Australian Acacias: an overview. Aus. Sys. Bot. 16(1), 89–102.

  • Miller JT and Bayer RJ (2001) Molecular phylogenetics of Acacia (Fabaceae: Mimosoideae) based on the chloroplast matK coding sequence and flanking trnK intron spacer region. Am. J. Bot. 88(4), 697–705.

  • Miller JT and Bayer RJ (2003) Molecular Phylogenetics of Acacia subgenera Acacia and Aculeiferum (Fabaceae: Mimosoideae) based on the chloroplast matK coding sequence and flanking trnK intron spacer regions. Aus. Sys. Bot. 16, 27–33.

  • Miller JT, Grimes JW, Murphy DJ, Bayer RJ and Ladiges PY (2003) A phylogenetic analysis of the Acacieae and Ingeae (Mimosoideae: Fabaceae) based on trnK, matK, psbA-trnH, -and trnL/trnF sequence data. Sys. Bot. 28, 558-566.

  • Newmaster SG and Ragupathy S (2009a) Testing Plant Barcoding in a Sister Species Complex of Pantropical Acacias (Mimosoideae, Fabaceae). Molecular Ecological Resources. 9(Suppl. 1), 172–180. (doi: 10.1111/j.1755-0998.2009.02642.x).

  • Newmaster SG and Ragupathy S (2009b) Ethnobotany Genomics – Discovery and Innovation in a New Era of Exploratory Research. J. Ethnobiol. Ethnomedicine. (in review).

  • Newmaster SG, Fazekas A and Ragupathy S (2006b) DNA barcoding in the land plants: evaluation of rbcl in a multigene tiered approach. Can. J. Bot. 84, 335-341.

  • Newmaster SG, Fazekas A, Steeves R and Janovec J (2008b) Testing Candidate Plant Barcode Regions in the Myristicaceae. Mol. Ecol. Res. 8, 480–490.

  • Newmaster SG, Murugesan M, Ragupathy S, Nagaraj N and Velusamy B (2009b) Ethnobotany Genomics study reveals three new species from the Velliangiri Hills in the Nilgiri Biosphere Reserve, Western Ghats, India. Ethnobot. 21, 1-28.

  • Newmaster SG, Ragupathy S and Janovec J (2009a) A Botanical Renaissance: State-of-the-art DNA Barcoding Facilitates an Automated Identification Technology (AIT) System for Plants. International Journal of Computer Applications in Technology. (Invited article, in press).

  • Newmaster SG, Ragupathy S, Balasubramaniam NC, and Ivanoff RF (2007) The Multi-mechanistic Taxonomy of The Irulas In Tamil Nadu, South India. J. Ethnobiol. 27, 31-44.

  • Newmaster SG, Ragupathy S, Ivanoff RF, and Nirmala CB (2006a) Mechanisms of Ethnobiological Classification. Ethnobot.. 18(1,2), 4-26.

  • Newmaster SG, Velusamy B, Murugesan M and Ragupathy S (2008a) Tripogon cope, a new species of Tripogon (Poaceae: Chloridoideae) in India with a Morphometric analysis and synopsis of Tripogon in India. Sys. Bot. 33(4), 695–701.

  • Pennisi E (2007) Wanted: a barcode for plants. Science. 318, 190–191.

  • Ragupathy S and Newmaster SG (2009b) Valorizing the 'Irulas' traditional knowledge of medicinal plants in the Kodiakkarai Reserve Forest, India. J. Ethnobiol. Ethnomedicine. 5(10), 1-13.

  • Ragupathy S, Ashwath N and Mahadevan A (1997) Acacias and mine rehabilitation: the need for inoculating acacias with mycorrhizal fungi, Forestry Program, ACIAR Acacia Publication, Australia. In: Turnbull, J. W., H.R. Crompton and K. Pinyopusarerk. eds. Recent Developments in Acacia Planting. Proceedings of an International workshop held in Hanoi, Vietnam, Australian Centre for International Agricultural Research, Canberra. pp. 274-280.

  • Ragupathy S, Newmaster SG, Gopinadhan P and Newmaster C (2008b) Exploring Ethnobiological Classifications for Novel Alternative Medicine: a case study of Cardiospermum halicacabum L. (Modakathon, Balloon Vine) as a traditional herb for treating rheumatoid arthritis. Ethnobot. 19, 1–20.

  • Ragupathy S, Newmaster SG, Murugesan M, Velusamy B and Huda M (2008) Consensus of the 'Malasars' traditional aboriginal knowledge of medicinal plants in the Velliangiri holy hills, India. J. Ethnobiol. Ethnomedicine. 4(8), 1-14.

  • Ragupathy S, Newmaster SG, Velusamy B and Murugesan M (2009a) DNA barcoding discriminates a new cryptic grass species revealed in an ethnobotany study by the hill tribes of the Western Ghats in southern India. Mol. Ecol. Res. 9(Suppl. l), 172–180.

  • Ratnasingham S and Hebert PDN (2007) BOLD: the Barcode of Life Data System (www.barcodinglife.org). Mol. Ecol. Notes. 7(3), 355–364.

  • Rodan BD, Newton AC and Verissimo A (1992) Mahogany conservation: status and policy initiatives. Environ. Conservation. 19, 331-338.

  • Rohlf F (2000) NTSYS: Numerical Taxonomy and Multivariate Analysis System, Version 2.1. Exeter Software, New York.

  • Ross JH (1981) An analysis of the African Acacia species: their distribution, possible origins and relationships. Bothalia. 13, 389–413.

  • Sauquet H, Doyle JA, Scharaschkin T et al. (2003) Phylogenetic analysis of Magnoliales and Myristicaceae based on multiple data sets: implications for character evolution. Bot. J. Linnean Soc. 142, 125–186.

  • Seigler DS, Ebinger JE and Miller JT (2006) The genus Senegalia (Fabaceae: Mimosoideae) from the New World. Phytologia. 88(1), 38–93.

  • Smith AC (1937) The American species of the Myristicaceae. Brittonia. 2, 393–510.

  • Sneath P and Sokal R (1973) Numerical taxonomy. W. H. Freeman, San Francisco, California, USA

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

  • Tautz D, Arctander P, Minelli, A, Thomas RH and Vogler AP (2002) DNA points the way ahead in taxonomy. Nature. 418, 479.

  • Trotter R and Logan M (1986) Informant consensus: a new approach for identifying potentially effective medicinal plants. In: Plants in indigenous medicine and diet: biobehavioural approaches (ed. Etkin NL), pp.234 91-112. Redgrave Publishers, Bedfort Hills, NY.

  • Van Gils C and Cox PA (1994) Ethnobotany of nutmeg in the Spice Islands. J. Ethnopharmacol. 42, 117-124.

  • Wardill TJ, Graham GC, Zalucki M et al. (2005) The importance of species identity in the biocontrol process: identifying the subspecies of Acacia nilotica (Leguminosae: Mimosoideae) by genetic distance and the implications for biological control. J. Biogeography. 32, 2145–2159.

  • Wheeler QD, Raven PH and Wilson EO (2004) Taxonomy: Impediment or Expedient? Science. 303(5656), 285-286.

  • Wickens GE, Seif-El-Din AG, Sita G and Nahal I (1995) Role of Acacia species in the rural economy of dry Africa and the Near East. FAO Conservation Guide No. 27. Food and Agriculture Organization, Rome, Italy.

  • Wight R and Arnott GAW (1834) Prodromus Florae Peninsulae Indiae Orientalis. London.

  • Will KW and Rubinoff D (2004) Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics. 20, 47–55.


Abstract Views: 372

PDF Views: 108




  • Ethnobotany Genomics - Use of DNA Barcoding to Explore Cryptic Diversity in Economically Important Plants

Abstract Views: 372  |  PDF Views: 108

Authors

Steven G. Newmaster
Biodiversity Institute of Ontario Herbarium, University of Guelph, Guelph, Ontario, Canada. N1G 2W1, Canada
Subramanyam Ragupathy
Biodiversity Institute of Ontario Herbarium, University of Guelph, Guelph, Ontario, Canada. N1G 2W1, Canada

Abstract


The ethnobotany genomics concept is founded on the idea of 'assemblage' of biodiversity knowledge. This includes a coming together of different ways of knowing and valorizing species variation in a novel approach seeking to add value to both traditional knowledge (TK) and scientific knowledge (SK). Ethnobotany genomics is defined as exploring the variation in genomic sequences from many species, and here we present some of our recent work that demonstrates the potential benefits of this approach for ethnobotanical research with economic implications. DNA barcoding was used to identify Acacia and nutmeg taxa that are economically important to society-at-large. Furthermore we identified considerable variation that is recognized by several indigenous cultures. The impacts of ethnobotany genomics will extend well beyond biodiversity science. Explorations of the genomic properties across the expanse of life are now possible using DNA barcoding to assemble sequence information for a standard portion of the genome from large assemblages of species. Perhaps the most important contribution is major barcode projects will leave an important legacy; a comprehensive repository of highquality DNA extracts that will facilitate future genomic investigations.

Keywords


DNA Barcoding, Economic Botany, Biodiversity, Plant Diversity, Ethnopharmacology,Ethnomedicine, Ethnobiology, Biotechnology

References





DOI: https://doi.org/10.17485/ijst%2F2009%2Fv2i5%2F29456