Journal of Genetics

, 98:100 | Cite as

Narrow gene pool can threaten the survival of Calamus nagbettai R. R. Fernald & Dey: a highly, endemic dioecious rattan species in the Western Ghats of India

  • Suma Arun DevEmail author
  • Swathi Balakrishnan
  • Anoja Kurian
  • V. B. Sreekumar
Research Article


Rattans, the spiny climbing palms of Arecaceae (Palmae) family exhibit high endemism to the biodiversity hot spots in India. Of the five rattan genera, Calamus is the only genus found in peninsular India with 15 of 21 species, endemic to the Western Ghats. The extensive utilization of rattans owing to their strength, durability and huge demand has resulted in depletion of their natural resources. Of the 15 endemic species, C. nagbettai is the most affected species on account of endemism, low population size and restricted distribution with fragmented populations. The present study revealed high amount of genetic diversity in the surviving scattered populations of the species using microsatellite markers. High gene flow (Nm = 1.498) observed across the populations resulted in low genetic differentiation (14%). A clear genetic admixture could be seen in Kerala as well as one of the Karnataka’s populations while the remaining two populations were genetically distinct. UPGMA, PCoA and STRUCTURE analyses showed significantly different genetic composition in Kerala population compared to other populations. Kerala and Karnataka populations of C. nagbettai were also unique in their genetic structure and allelic composition. Therefore, effective management and conservation strategies have to be implemented to preserve the rare alleles with adaptive potential to protect this economically valuable Calamus species from endangerment. Overexploitation, low seed set and poor regeneration, as well as habitat fragmentation can further threaten the survival of this endemic, narrowly distributed dioecious rattan species in the Western Ghats region.


rattans overexploitation simple sequence repeat genetic diversity conservation. 



We are grateful to the Director, KFRI and the Kerala Forest Department (KFD), Govt. of Kerala for encouragement and permission to collect plant samples from reserve forests as well as protected areas. The financial support received from Kerala State Council for Science, Technology and Environment (KSCSTE), Govt. of Kerala is gratefully acknowledged.


  1. Agren J., Elmqvist T. and Tunlid A. 1986 Pollination by deceit, floral sex ratio and seed set in dioecious Rubus Chamaemorus L. Oecoligia 70, 332–338.CrossRefGoogle Scholar
  2. Ahmedullah M. and Nayar M. P. 1986 Endemic plants of the Indian region, vol. 1, pp. 190–194. Botanical survey of India, Howrah.Google Scholar
  3. Barrett S. C. H. and Kohn J. R. 1991 Genetic and evolutionary consequences of small population size in plants: implication for conservation. In Genetics and conservation of rare plants (ed. D. A. Falk and K. E. Holsinger), pp. 3–30. Oxford University Press, Oxford.Google Scholar
  4. Bartish I. V., Jeppsson N. and Nybom H. 1999 Population genetic structure in the dioecious pioneer plant species Hippophae rhamnoides investigated by random amplified polymorphic DNA (RAPD) markers. Mol. Ecol. 8, 791–802.CrossRefGoogle Scholar
  5. Basu S. K. 1992 Rattans (Canes) in India - a monographic revision. Rattan information Centre, Kepong, Kuala Lumpur.Google Scholar
  6. Billotte N. 2001 Development, characterization, and across-taxa utility of oil palm (Elaeis guinensis Jacq.) microsatellite markers. Genome 44, 413–425.PubMedCrossRefGoogle Scholar
  7. Billotte N., Marseillac N., Brottier P., Noyer J. L., Collet J. P., Moreau C. et al. 2004 Nuclear microsatellite markers for the date palm (Phoenix dactylifera L.) - Characterization and utility across the genus Phoenix and in other palm genera. Mol. Ecol. Notes 4, 256–258.CrossRefGoogle Scholar
  8. Bon M. C. 1995 Isozyme of rattan species and their genetic interpretation. Electrophoresis 17, 1248–1252.CrossRefGoogle Scholar
  9. Brown A. H. D. 1992 Human impact on plant gene pools and sampling for their conservation. Biol. Con. 62, 144.CrossRefGoogle Scholar
  10. Carlsson-Graner U., Elmqvisy T., Agren J., Gardfiell H. and Ingvarsson P. 1998 Floral sex ratio, diseases and seed set in dioecious Silene dioica. J. Ecol. 86, 79–91.CrossRefGoogle Scholar
  11. Chandran M. D. S. 1997 On the ecological history of the Western Ghats. Curr. Sci. 73, 146–155.Google Scholar
  12. Chen C. and Okie W. R. 2015 Novel peach flower types in a segregating population from ‘Helen Borchers’. J. Am. Soc. Hortic. Sci. 140, 172–177.CrossRefGoogle Scholar
  13. Doyle J. J. and Doyle J. L. 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11–15.Google Scholar
  14. Earl G. 2012 STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359–363.CrossRefGoogle Scholar
  15. Ellstrand N. C. and Elam D. R. 1993 Population genetic consequences of small population size: implications for plant conservation. Annu. Rev. Ecol. Evol. Syst. 24, 217–242.CrossRefGoogle Scholar
  16. Elmqvist T., Liu D., Carlsson U. and Giles B. E. 1993 Anther –smut infection in Silene dioica: variation in floral morphology and patterns of spore deposition. Oikos 68, 207–216.CrossRefGoogle Scholar
  17. Elshibli S. and Korpelainen H. 2009 Biodiversity of date palms (Phoenix dactylifera L.) in Sudan: chemical, morphological and DNA polymorphisms of selected cultivars. Plant. Genet. Resour. 7, 194–203.CrossRefGoogle Scholar
  18. Evanno G., Regnaut S. and Goudet J. 2005 Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14, 2611–2620.PubMedCrossRefGoogle Scholar
  19. Forapani S., Carboni A., Paoletti C., Cristiana Moliterni V. M., Ranalli P. and Mandolino G. 2001 Comparison of hemp varities using random amplified polymorphic DNA markers. Crop. Sci. 41, 1682–1689.CrossRefGoogle Scholar
  20. Gerber S., Chadoeuf J., Gugerli F., Lascoux M., Buiteveld J., Cottrell J. et al. 2014 High rates of gene flow by pollen and seed in oak populations across Europe. PLoS One 9, e85130.PubMedPubMedCentralCrossRefGoogle Scholar
  21. Gibson J. P., Rice S. A. and Stucke C. M. 2008 Comparison of population genetic diversity between a rare, narrowly distributed species and a common, widespread species of Alnus (Betulaceae). Am. J. Bot. 95, 588–596.PubMedCrossRefGoogle Scholar
  22. Gilpin M. E. and Soulè M. E. 1986 Minimum viable populations: process of species extinction. In Conservation biology: the science of scarcity and diversity (ed. M. E. Soulè), pp. 19–35. Sinauer, Sunderland.Google Scholar
  23. Gitzendanner M. A. and Soltis P. S. 2000 Patterns of genetic variation in rare and widespread plant congeners. Am. J. Bot. 87, 783–792.PubMedCrossRefGoogle Scholar
  24. Govaerts R., Dransfield J., Zona S., Hodel D. R. and Henderson A. 2015 World checklist of Arecaceae. Royal Botanic Gardens, Kew.Google Scholar
  25. Hamrick J. L., Godt M. J. W., Murawski D. A. and Loveless M. D. 1991 Correlations between species traits and allozyme diversity: implications for conservation biology. In Genetics and conservation of rare plants (ed. D. A. Falk and K. E. Holsinger), pp. 75–86. Oxford University Press, New York.Google Scholar
  26. Hamrick J. L., Godt M. J. W. and Sherman-Broyles S. L. 1992 Factors influencing levels of genetic diversity in woody plant species. New Forest 6, 95–124.CrossRefGoogle Scholar
  27. Harris-Shultz K. R., Harrison M., Wald P., Trigiano R. N. and Rinehart T. 2014 Development and characterization of microsatellite markers for a little blue stem collection. J. Am. Soc. Hortic. Sci. 140, 78.CrossRefGoogle Scholar
  28. House S. M. 1992 Population density and fruit set in three dioecious tree species in Australian tropical rain forest. J. Ecol. 80, 57–69.CrossRefGoogle Scholar
  29. Jakobsson M. and Rosenberg N. A. 2007 CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23, 1801–1806.PubMedCrossRefPubMedCentralGoogle Scholar
  30. Jha C. S., Dutt C. B. S. and Bawa K. S. 2000 Deforestation and land use changes in Western Ghats, India. Curr. Sci. 79, 231–238.Google Scholar
  31. Joshi M. 2017 Assigning conservation value and identifying hotspots of endemic rattan diversity in the Western Ghats, India. Plant Divers. 39, 263–272.PubMedCrossRefPubMedCentralGoogle Scholar
  32. Jump A. S. and Penuelas J. 2005 Running to stand still: adaptation and the response of plants to rapid climate change. Ecol. Lett. 8, 1010–1020.CrossRefGoogle Scholar
  33. Kang M., Jiang M. and Huang H. 2005 Genetic diversity in fragmented populations of Berchemiella wilsonii var. pubipetiolata (Rhamnaceae). Ann. Bot. 95, 1145–1151.PubMedPubMedCentralCrossRefGoogle Scholar
  34. Kapteyn J. and Simon J. E. 2002 The use of RAPDs for assessment of identify, diversity and quality of Echinacea. In Trends in new crops and new uses (ed. J. Janick and A. Whipkey), pp. 509–513. ASHS Press, Alexandria.Google Scholar
  35. Karron J. D. 1991 Patterns of genetic variation and breeding systems in rare plant species. In Genetics and conservation of rare plants (ed. D. A. Ealk and K. I. C. Holsinger), pp. 87–98. Oxford University Press, New York.Google Scholar
  36. Kumbhar S. D., Kulwal P. L., Patil J. V., Sarawate C. D., Gaikwad A. P. and Jadhav A. S. 2015 Genetic diversity and population structure in landraces and improved rice varieties from India. Rice Sci. 22, 99–107.CrossRefGoogle Scholar
  37. Kurian B. and Sabu K. K. 2017 Microsatellite markers reveal male-specific DNA sequences in Calamus thwaitesii, an important economic rattan palm. Theoret. Appl. Sci. 9, 181–185.Google Scholar
  38. Kurian B., Varghese V., Nair V. V., Hemanth Kumar A. S. and Sabu K. K. 2013 Analysis of genetic diversity in an economic rattan palm, Calamus thwaitesii Becc. using SSR and ISSR markers. In Proceedings of the National Seminar on Tree Biotechnology (ed. Modhumita Dasgupta, Rekha R. Warrier and R. Yasodha), pp. 226–228. Institute of Forest Genetics and Tree Breeding, Coimbatore.Google Scholar
  39. Kurian B., Hemanthakumar A. S., Jacob J., Noushad M. A. and Sabu K. K. 2018a Rapidly evolving sex-specific sequences in Calamus travancoricus Bedd. ex. Becc. and Calamus nagbettai R.R. Fernald & Dey. Tree Genet. Genomics 14, 11.Google Scholar
  40. Kurian B., Hemanthakumar A. S., Jacob J., Ratnam W., Choong C. Y. and Sarmah P. et al. 2018b Intraspecific genetic variability, differentiation and evolutionary relationships revealed through microsatellite loci in seven economically important Calamus species. J. For. Res. 30, 1–13.Google Scholar
  41. Lakshmana A. C. 1993 Rattans of south India, pp. 180–188. Evergreen Publishers, Bengaluru.Google Scholar
  42. Lewontin R. C. 1972 Testing the theory of natural selection. Nature 236, 181–182.CrossRefGoogle Scholar
  43. Li C. and Luukkanen O. 2001 Genetic diversity in natural populations of Eucalyptus microtheca. European Tropical Forest Research Network. ETFRN News 34, 18–19.Google Scholar
  44. Li F., Yang F., Weng Q., Yin G., Li M. and Gan S. 2013 Generation and analysis of expressed sequence tags for microsatellite marker development in Calamus simplificolius C.F Wei. Mol. Breed. 31, 867–877.CrossRefGoogle Scholar
  45. Liu K. and Muse S. V. 2005 PowerMarker: an intergrtaed analysis environment or genetic marker analysis. Bioinformatics 21, 2128–2129.PubMedCrossRefGoogle Scholar
  46. Loveless M. D. and Hamrick J. L. 1984 Ecological determinants of genetic structure in plant populations. Annu. Rev. Ecol. Syst. 15, 65–95.CrossRefGoogle Scholar
  47. Lowe A., Harris S. and Ashton P. 2004 Ecological genetics: design, analysis, and application, pp. 344. Wiley-Blackwell, Malden.Google Scholar
  48. Lyngdoh N., Santhosh S. H., Ramesha B. T., Nageswara Rao M., Ravikanth G., Narayani B. et al. 2005 Rattan species richness and population genetic structure of Calamus flagellum in north-eastern Himalaya India. J. Bamboo Rattan 4, 293–307.CrossRefGoogle Scholar
  49. Manohara T. N., Ramaswamy S. N. and Shivamurthy G. R. 2007 Calamus dwindling resources? Curr. Sci. 92, 290–292.Google Scholar
  50. Mason A. S. 2015 SSR Genotyping. In Plant genotyping (ed. J. Batley), pp. 77–89. Springer, New York.CrossRefGoogle Scholar
  51. Matesanz S., Rubio Teso M. L., García-Fernández A. and Escudero A. 2017 Habitat fragmentation differentially affects genetic variation, phenotypic plasticity and survival in populations of a gypsum endemic. Front Plant Sci. 8, 843.PubMedPubMedCentralCrossRefGoogle Scholar
  52. McDermott J. A. and McDonald B. A. 1993 Gene flow in plant pathosystems. Ann. Rev. Phytopathol. 31, 353–373.CrossRefGoogle Scholar
  53. Meena R. K., Raj H., Sharma P., Yadav S., Kant R. and Bhandari M. S. 2018. Assessment of genetic diversity in natural populations of Calamus guruba Buch. - Ham. ex Mart. using ISSR marker. Trop. Plant Res. 5, 250–259.CrossRefGoogle Scholar
  54. Meerow A. W., Wisser R. J., Brown J. S., Kuhn D. N., Schnell R. J. and Broschat T. K. 2003 Analysis of genetic diversity and population structure within Florida coconut (Cocos nucifera L.) using microsatellite DNA with special emphasis on the Fiji Dwarf cultivar. Theor. Appl. Genet. 106, 715–726.PubMedCrossRefGoogle Scholar
  55. Peakall R. and Smouse P. E. 2006 GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6, 288–295.CrossRefGoogle Scholar
  56. Perera L., Russell J. R., Provan J. and Powell W. 2000 Use of microsatellite DNA markers to investigate the level of genetic diversity and population genetic structure of coconut (Cocos nucifera L). Genome 43, 15–21.PubMedCrossRefGoogle Scholar
  57. Pritchard J. K., Wen X. and Falush D. 2010 Documentation for SRTUCTURE software, version 2.3. University of Chicago, Chicago.Google Scholar
  58. Priya K., Indira E., Sreekumar V. B. and Renuka C. 2016 Assessment of genetic diversity in Calamus vattayila Renuka (Arecaceae) using ISSR markers. J. Bamboo Rattan 15, 61–69.Google Scholar
  59. Ramesha B. T., Ravikanth G., Nageswara Rao M., Ganeshaiah K. N. and Uma Sahaanker R. 2007 Genetic structure of the rattan Calamus thwaitesii in core, buffer and peripheral regions of three protected areas in central Western Ghats, India: do protected areas serve as refugia for genetic resources of economically important plants? J. Genet. 86, 9–18.PubMedCrossRefGoogle Scholar
  60. Rao N., Ramesha B. T., Ravikanth G., Ganeshaiah K. N. and Shaanker R. U. 2007 Cross-species amplification of coconut microsatellite markers in Rattans. Silvae Genet. 56, 282–286.CrossRefGoogle Scholar
  61. Rattanland 2011 The rattan industry at a glance. Accessed 11 January 2011 (
  62. Ravikanth G., Ganeshaiah K. N., Uma Shaanker R. and Shaanker R. U. 2001 Mapping genetic diversity of rattans in the Central Western Ghats: Identification of hot-spots of variability for in situ conservation. In Forest genetic resources: status, threats and conservation strategies (ed. R. Uma Shaanker, K. N. Ganeshaiah and K. S. Bawa), pp 69–83. Science Publishers, Enfield, NH, USA.Google Scholar
  63. Ravikanth G., Uma Shaanker R. and Ganeshaiah K. N. 2002 Identification of hot spots of species richness and genetic variability in rattans: an approach using geographical information systems (GIS) and molecular tools. Plant Genet. Resour. Newsl. 132, 17–21.Google Scholar
  64. Ravikanth G., Nageswara Rao M., Narwade A., Uma Shaanker R. and Ganeshaiah K. N. 2010 Do endemic rattans have lower genetic variability than their co-generic and con-specific non-endemic rattans? Genes, Genomes & Genomics 4, 22–27.Google Scholar
  65. Renuka C. 1992 Rattans of Western Ghats. A taxonomic Manual, KFRI, Peechi, Kerala.Google Scholar
  66. Renuka C. 1995 A Manual of the Rattans of Andaman and Nicobar Islands. KFRI, Peechi, Kerala.Google Scholar
  67. Renuka C. 1999 Indian rattan distribution – an update. Indian For. 25, 591–598.Google Scholar
  68. Renuka C. and Sreekumar V. B. 2012 A Field guide to the palms of India. Kerala Forest Research Institute, Peechi, Thrissur, Kerala.Google Scholar
  69. Renuka C., Indira E. P. and Muralidharan E. M. 1998 Genetic diversity and conservation of certain species of Calamus in Andaman and Nicobar Islands and Southern India. KFRI Res. Rep. 157, 25.Google Scholar
  70. Rosenberg N. A. 2004 DISTRUCT: a program for the graphical display of population structure. Mol. Ecol. Notes 4,137–138.CrossRefGoogle Scholar
  71. Sarmah P. and Sarma R. N. 2011 Identification of a DNA marker linked to sex determination in Calamus tenuis Roxb., an economically important rattan species in northeast India. Mol. Breed. 27, 115–118.CrossRefGoogle Scholar
  72. Sarmah P., Barua V. J., Nath J., Sarma R. N., Kurian B., Hemanthkumar A. S. et al. 2016 ISSR and SSR markers reveal sex-specific DNA sequences in three Calamus species from India. Agrofor. Syst. 91, 509–513.CrossRefGoogle Scholar
  73. Selkoe K. A. and Toonen R. J. 2006 Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol. Lett. 9, 615–629.PubMedCrossRefPubMedCentralGoogle Scholar
  74. Singh B. H., Puni L., Jain A. and Rao P. G. 2004 Status, utility, threats and conservation options for rattan resources in Manipur. Curr. Sci. 87, 90–94.Google Scholar
  75. Sinha P., Bal P. and Panda P. C. 2018 Assessment of genetic diversity among six species of Calamus (Arecaceae) in Eastern Ghats of India using molecular markers. IJISRT 3, 656–668.Google Scholar
  76. Smith D. N. and Devey M. E. 1994 Occurrence and inheritance of microsatellites in Pinus radiata. Genome 37, 977–983.PubMedCrossRefGoogle Scholar
  77. Sreekumar V. B. and Renuka C. 2006 Assessment of genetic diversity in Calamus thwaitesii Becc. (Arecaceae) using RAPD markers. Biochem. Syst. Ecol. 34, 397–405.CrossRefGoogle Scholar
  78. Sreekumar V. B., Renuka C., Suma T. B. and Balasundaran M. 2006 Taxonomic reconsideration of Calamus rivalis Thw. ex Trim. And C. metzianus Schlecht (Arecaceae) through morphometric and molecular analyses. Bot. Stud. 47, 443–452.Google Scholar
  79. Teulat B., Adam R., Trehin P., Lebrun J. H. A., Barker G. M., Arnold G. M. et al. 2000 An analysis of genetic diversity in coconut (Cocos nucifera) population from across the geographical range using sequence tagged microsatellites (SSRs) and AFLPs. Theor. Appl. Genet. 100, 764–771.CrossRefGoogle Scholar
  80. Uhl N. and Dransfield J. 1987 Genera Palmarum. Allen Press, Lawrence.Google Scholar
  81. Uma Shaanker R., Ganeshaiah K. N., Srinivasan K., Ramanantha R. V. and Hong L. T. 2004 Bamboos and rattans of the Western Ghats: population biology, socio-economic and conservation strategies. ATREE Publications, Bengaluru.Google Scholar
  82. Wachira F. N., Waugh R., Hackett C. A. and Powell W. 1995 Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers. Genome 38, 201–210.PubMedCrossRefGoogle Scholar
  83. Willi Y., Van Buskirk J. and Hoffmann A. A. 2006 Limits to the adaptive potential of small populations. Ann. Rev. Ecol. Syst. 37, 433–458.CrossRefGoogle Scholar
  84. Wright S. 1969 Evolution and genetics of populations. In The theory of gene frequencies, vol. 27, pp. 758–760. University of Chicago Press, Chicago.Google Scholar
  85. Yeh F. C., Boyle T. and Yang R. C. 1999 Microsoft Window-based freeware for population genetic analysis (POPGENE) ver.1.31. University of Alberta, Edmonton.Google Scholar
  86. Young A., Boyle T. and Brown T. 1996 The population genetic consequences of habitat fragmentation for plants. Trends Ecol. Evol. 11, 413–418.PubMedCrossRefGoogle Scholar
  87. Zhang H. J., Qu L. J., Xiang C., Xia J. F., Gao Y. M. and Shi Y. Y. 2014 Dissection of genetic mechanism of abnormal heading in hybrid rice. Rice Sci. 21, 201–209.CrossRefGoogle Scholar
  88. Zong J. W., Zhao T. T., Ma Q. H., Liang L. S. and Wang G. X. 2015 Assessment of genetic diversity and population genetic structure of Corylus mandshurica in China using SSR markers. PLoS One 109, e0137528.CrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  1. 1.Forest Genetics and Biotechnology DivisionKerala Forest Research InstitutePeechi, ThrissurIndia
  2. 2.Forest Ecology and Biodiversity Conservation DivisionKerala Forest Research InstitutePeechi, ThrissurIndia

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