Plant Systematics and Evolution

, Volume 300, Issue 1, pp 1–12 | Cite as

Phylogeography of a rare orchid, Vexillabium yakushimense: comparison of populations in central Honshu and the Nansei Island chain, Japan

  • Ikuyo Saeki
  • Asako Kitazawa
  • Atsushi Abe
  • Koya Minemoto
  • Fumito Koike
Original Article

Abstract

Vexillabium yakushimense is a rare, terrestrial orchid which occurs in east and southeast Asia. In spite of its inconspicuous appearance, several new populations were discovered in central Honshu, Japan. Because these populations are geographically isolated at its northern range limit of distribution, they were suspected to have distinctive genetic characteristics. Given this hypothesis, we quantified the genetic variation of V. yakushimense for populations of central Honshu, and the Nansei Island chain, which represent the most southern locality in Japan. Leaves were collected from nine populations in central Honshu (n = 48) and two populations from the Nansei Island chain (n = 29). We examined genetic variation using cpDNA (1,205 bp) and ITS (511 bp) markers. Based on the cpDNA variation, a total of seven haplotypes were recovered; populations in central Honshu were clearly differentiated from those in the Nansei Island chain. Relatively high allelic richness and haplotype diversity were found in the pooled population of central Honshu. These populations likely maintained an adequate population size for a long period despite a markedly different ecological niche compared to that in the Nansei Island chain. In contrast to cpDNA, little variation was detected in ITS. Further studies on geographic occurrences, reproductive biology and mycorrhizal association are encouraged for its conservation.

Keywords

Biogeography Chloroplast DNA Disjunct distribution Endangered species Genetic diversity 

References

  1. Alexander C, Alexander IJ, Hadley G (1984) Phosphate-uptake by Goodyera repens in relation to mycorrhizal infection. New Phytol 97(3):401–411CrossRefGoogle Scholar
  2. Arditti J, Ghani AKA (2000) Numerical and physical properties of orchid seeds and their biological implications. New Phytol 146(3):569CrossRefGoogle Scholar
  3. Cameron DD, Leake JR, Read DJ (2006) Mutualistic mycorrhiza in orchids: evidence from plant–fungus carbon and nitrogen transfers in the green-leaved terrestrial orchid Goodyera repens. New Phytol 171(2):405–416PubMedCrossRefGoogle Scholar
  4. Cribb PJ, Kell SP, Dixon KW, Barrett RL (2003) Orchid conservation: a global perspective. In: Dixon KW, Kell SP, Barrett RL, Cribb PJ (eds) Orchid conservation. Natural History Publications, Kota Kinabalu, pp 1–24Google Scholar
  5. Dearnaley JDW (2007) Further advances in orchid mycorrhizal research. Mycorrhiza 17(6):475–486PubMedCrossRefGoogle Scholar
  6. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochem Bull 19:11–15Google Scholar
  7. Dressler RL (1993) Phylogeny and classification of the orchid family. Dioscorides Press, PortlandGoogle Scholar
  8. Duffy KJ, Scopece G, Cozzolino S, Fay MF, Smith RJ, Stout JC (2009) Ecology and genetic diversity of the dense-flowered orchid, Neotinea maculata, at the centre and edge of its range. Ann Bot 104(3):507–516PubMedCrossRefGoogle Scholar
  9. Eckert CG, Samis KE, Lougheed SC (2008) Genetic variation across species’ geographical ranges: the central-marginal hypothesis and beyond. Mol Ecol 17(5):1170–1188PubMedCrossRefGoogle Scholar
  10. Ehime Prefecture (2003) Red data book Ehime. Ehime Prefecture, JapanGoogle Scholar
  11. Ek RC, Ter Steege H, Biesmeijer KC (1997) Vertical distribution and association of vascular epiphytes in four different forest types in the Guianas. In: Ek RC (ed) Botanical diversity in the tropical rain forest of Guyana, Ph.D. thesis. Utrecht University, The Netherlands, pp 65–89Google Scholar
  12. El Mousadik A, Petit RJ (1996) Chloroplast DNA phylogeography of the argan tree of Morocco. Mol Ecol 5(4):547–555PubMedCrossRefGoogle Scholar
  13. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes—application to human mitochondrial-DNA restriction data. Genetics 131(2):479–491PubMedGoogle Scholar
  14. Fenster CB, Armbruster WS, Wilson P, Dudash MR, Thomson JD (2004) Pollination syndromes and floral specialization. Ann Rev Ecol Evol Syst 35:375–403CrossRefGoogle Scholar
  15. Forrest AD, Hollingsworth ML, Hollingsworth PM, Sydes C, Bateman RM (2004) Population genetic structure in European populations of Spiranthes romanzoffiana set in the context of other genetic studies on orchids. Heredity 92(3):218–227Google Scholar
  16. Frankham R (1997) Do island populations have less genetic variation than mainland populations? Heredity 78:311–327PubMedCrossRefGoogle Scholar
  17. GBIF (2012) Global Biodiversity Information Facility. Available via http://www.gbif.org/ Accessed 2012.8.1
  18. Gentry AH, Dodson CH (1987) Diversity and biogeography of neotropical vascular epiphytes. Ann Mo Bot Gard 74(2):205–233CrossRefGoogle Scholar
  19. Gravendeel B, Smithson A, Slik FJ, Schuiteman A (2004) Epiphytism and pollinator specialization: drivers for orchid diversity? Philos Trans R Soc London Ser B Biol Sci 359(1450):1523–1535CrossRefGoogle Scholar
  20. Hampe A, Petit RJ (2005) Conserving biodiversity under climate change: the rear edge matters. Ecol Lett 8(5):461–467PubMedCrossRefGoogle Scholar
  21. Hatsushima S (1971) Flora of the Ryukyus: including Amami islands, Okinawa islands, and Sakishima archipelago. Okinawa-seibutsu-kyouiku-kenkyuukai, OkinawaGoogle Scholar
  22. Inoue K (1996) Present status and conservation of orchids in Japan. Jap J Conserv Ecol 1:115–129 (in Japanese with English abstract)Google Scholar
  23. Ishikawa N, Yokoyama J, Ikeda H, Takabe E, Tsukaya H (2006) Evaluation of morphological and molecular variation in Plantago asiatica var. densiuscula, with special reference to the systematic treatment of Plantago asiatica var. yakusimensis. J Plant Res 119(4):385–395PubMedCrossRefGoogle Scholar
  24. Johansson DR (1974) Ecology of vascular epiphytes in West African rain forests. Acta Phytogeographica Suecica 59:1–136Google Scholar
  25. Kew Royal Botanic Gardens (2013) World check list of selected plant families. Available via Kew Royal botanic Gardens. 2012. http://apps.kew.org/wcsp/advanced.do. Accessed January 22, 2013
  26. Kitazawa A (2009) Discovery of endangered plants in wetlands dominated by Acer pycnanthum. Bull Bot Soc Nagano 42:63–64Google Scholar
  27. Kitazawa A (2010) Discovery of endangered plants in wetlands dominated by Acer pycnanthum No. 2. Bull Bot Soc Nagano 43:55–58Google Scholar
  28. Kitazawa A (2011) Discovery of endangered plants in wetlands dominated by Acer pycnanthum No. 3. Bull Bot Soc Nagano 44:31–32Google Scholar
  29. Kitazawa A (2012) Discovery of endangered plants in wetlands dominated by Acer pycnanthum No. 3. Bull Bot Soc Nagano 45:39–41Google Scholar
  30. Kochi Prefecture (2009) Flora of Kochi. Kochi Prefecture, JapanGoogle Scholar
  31. Lawton JH (1993) Range, population abundance and conservation. Trends Ecol Evol 8(11):409–413PubMedCrossRefGoogle Scholar
  32. Lesica P, McCune B (2004) Decline of arctic-alpine plants at the southern margin of their range following a decade of climatic warming. J Veg Sci 15(5):679–690CrossRefGoogle Scholar
  33. Mabberley DJ (1997) The plant book. A portable dictionary of the vascular plants. 2nd edn. Cambridge University Press, CambridgeGoogle Scholar
  34. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27(2):209–220PubMedGoogle Scholar
  35. Matsushima N (1995) Morphogenetic history of the Ina Basin. Research Report of the Iida City Museum 3:1–145Google Scholar
  36. McCune B, Grace JB, Urban DL (2002) Analysis of ecological communities. MjM Software Design, Gleneden BeachGoogle Scholar
  37. McLachlan JS, Clark JS, Manos PS (2005) Molecular indicators of tree migration capacity under rapid climate change. Ecology 86(8):2088–2098CrossRefGoogle Scholar
  38. Micheneau C, Duffy KJ, Smith RJ, Stevens LJ, Stout JC, Civeyrel L, Cowan RS, Fay MF (2010) Plastid microsatellites for the study of genetic variability in the widespread Cephalanthera longifolia, C. damasonium and C. rubra (Neottieae, Orchidaceae), and cross-amplification in other Cephalanthera species. Bot J Linn Soc 163(2):181–193CrossRefGoogle Scholar
  39. Ministry of Environment (2012) Red list of vascular plants in Japan. Available via Ministry of Environment. http://www.biodic.go.jp/rdb/rdb_f.html. Accessed Sept 30, 2012
  40. Nakajima M (2012) Illustrations of Japanese Orchids. Bun-ichi Sogo Shuppan Co., TokyoGoogle Scholar
  41. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  42. Nieder J (2004) Distribution patterns of epiphytic orchids—present research, past causes and future consequences. In: Hermans J, Cribb P (ed) The European Orchid Conference and Show, London, London, 2003. The British Orchid Council and the Royal Horticultural Society, London, pp 241–258Google Scholar
  43. Nishizawa T, Watano Y (2000) Primer pairs suitable for PCR-SSCP analysis of chloroplast DNA in angiosperms. J Phytogeog Taxon 48:63–66Google Scholar
  44. Otero JT, Flanagan NS, Herre EA, Ackerman JD, Bayman P (2007) Widespread mycorrhizal specificity correlates to mycorrhizal function in the neotropical, epiphytic orchid Ionopsis utricularioides (Orchidaceae). Am J Bot 94(12):1944–1950PubMedCrossRefGoogle Scholar
  45. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6(1):288–295CrossRefGoogle Scholar
  46. Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12(4):844–855CrossRefGoogle Scholar
  47. Pillon Y, Chase MW (2007) Taxonomic exaggeration and its effects on orchid conservation. Conserv Biol 21(1):263–265PubMedCrossRefGoogle Scholar
  48. Ramirez SR, Eltz T, Fujiwara MK, Gerlach G, Goldman-Huertas B, Tsutsui ND, Pierce NE (2011) Asynchronous diversification in a specialized plant-pollinator mutualism. Science 333(6050):1742–1746PubMedCrossRefGoogle Scholar
  49. Roberts DL (2003) Pollination biology: the role of sexual reproduction in orchid conservation. In: Dixon KW, Kell SP, Barrett RL, Cribb PJ (eds) Orchid conservation. Natural History Publications, Kota KinabaluGoogle Scholar
  50. Saeki I, Murakami N (2009) Chloroplast DNA phylogeography of the endangered Japanese red maple (Acer pycnanthum): the spatial configuration of wetlands shapes genetic diversity. Divers Distrib 15:917–927CrossRefGoogle Scholar
  51. Sagarin RD, Gaines SD (2002) The ‘abundant centre’ distribution: to what extent is it a biogeographical rule? Ecol Lett 5:137–147CrossRefGoogle Scholar
  52. Sagarin RD, Gaines SD, Gaylord B (2006) Moving beyond assumptions to understand abundance distributions across the ranges of species. Trends Ecol Evol 21:524–530PubMedCrossRefGoogle Scholar
  53. Sang T, Crawford DJ, Stuessy TF (1997) Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). Am J Bot 84(8):1120–1136PubMedCrossRefGoogle Scholar
  54. Satake Y, Ohwi J, Kitamura S, Watari S, Tominari T (1985) Wild flowers of Japan, herbs. Heibonsha, TokyoGoogle Scholar
  55. Search System of Japanese Red Data (2012) Search System of Japanese Red Data. Available via http://jpnrdb.com/index.html. Accessed 1 Aug 2012 (in Japanese)
  56. Shimizu T (1997) Flora of Nagano prefecture. Shinano Mainichi Shinbun, NaganoGoogle Scholar
  57. Stone JL, Crystal PA, Devlin EE, Downer RH, Cameron DS (2012) Highest genetic diversity at the northern range limit of the rare orchid Isotria medeoloides. Heredity 109:215–221PubMedCrossRefGoogle Scholar
  58. Suetsugu K, Honda T (2012) New record of Vexillabium yakushimense from Kinki district. Bunrui 12(1):59–61Google Scholar
  59. Swarts ND, Dixon KW (2009a) Perspectives on orchid conservation in botanic gardens. Trends Plant Sci 14(11):590–598PubMedCrossRefGoogle Scholar
  60. Swarts ND, Dixon KW (2009b) Terrestrial orchid conservation in the age of extinction. Ann Bot 104(3):543–556PubMedCrossRefGoogle Scholar
  61. Takahashi S, Furukawa T, Asano T, Terajima Y, Shimada H, Sugimoto A, Kadowaki K (2005) Very close relationship of the chloroplast genomes among Saccharum species. Theor Appl Genet 110(8):1523–1529PubMedCrossRefGoogle Scholar
  62. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596–1599PubMedCrossRefGoogle Scholar
  63. Tate JA, Simpson BB (2003) Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species. Syst Bot 28(4):723–737Google Scholar
  64. Taylor DL, Bruns TD, Szaro TM, Hodges SA (2003) Divergence in mycorrhizal specialization within Hexalectris spicata (Orchidaceae), a nonphotosynthetic desert orchid. Am J Bot 90(8):1168–1179PubMedCrossRefGoogle Scholar
  65. The Environment Agency (2000) Threatened Wildlife of Japan, Red Data Book, Vascular Plants, vol 8. 2nd edn. Japan Wildlife Research Center, TokyoGoogle Scholar
  66. Tomaru N, Takahashi M, Tsumura Y, Uchida K, Ohba K (1997) Genetic diversity in Fagus crenata (Japanese beech): influence of the distributional shift during the late-quaternary. Heredity 78(3):241–251CrossRefGoogle Scholar
  67. Tremblay RL (1992) Trends in the pollination ecology of the Orchidaceae—evolution and systematics. Can J Bot 70(3):642–650CrossRefGoogle Scholar
  68. Ueda K (1989) Phytogeography of Tokai hilly land element I. Definition. Acta Phytotaxonomica Geobotanica 40:190–202Google Scholar
  69. Ueda K (1994) The origin and evolution of the Tokai hilly land element. In: Okada H, Ueda K, Kadono Y (eds) Natural history of plants: evolutionary studies of diversity. Hokkaido University Press, Sapporo, pp 3–18Google Scholar
  70. Urbatsch LE, Baldwin BG, Donoghue MJ (2000) Phylogeny of the coneflowers and relatives (Heliantheae: Asteraceae) based on nuclear rDNA internal transcribed spacer (ITS) sequences and chloroplast DNA restriction site data. Syst Bot 25(3):539–565CrossRefGoogle Scholar
  71. Vucetich JA, Waite TA (2003) Spatial patterns of demography and genetic processes across the species’ range: null hypotheses for landscape conservation genetics. Conserv Genet 4(5):639–645CrossRefGoogle Scholar
  72. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, San Diego, pp 315–322Google Scholar
  73. Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear Dnas. Proc Natl Acad Sci USA 84(24):9054–9058PubMedCrossRefGoogle Scholar
  74. Yamamoto Y (1924) Eine neue Art von Anoectochilus. Bot Mag 38:131–133Google Scholar
  75. Yoder JA, Zettler LW, Stewart SL (2000) Water requirements of terrestrial and epiphytic orchid seeds and seedlings, and evidence for water uptake by means of mycotrophy. Plant Sci 156(2):145–150PubMedCrossRefGoogle Scholar
  76. Yonekura K (2012) An enumeration of the vascular plants of Japan. Hokuryukan, TokyoGoogle Scholar

Copyright information

© Springer-Verlag Wien 2013

Authors and Affiliations

  • Ikuyo Saeki
    • 1
    • 2
    • 3
    • 6
  • Asako Kitazawa
    • 3
  • Atsushi Abe
    • 4
  • Koya Minemoto
    • 4
  • Fumito Koike
    • 5
  1. 1.Network Center of Forest and Grassland SurveyMonitoring Site 1000 Project, Japan Wildlife Research CenterTokyoJapan
  2. 2.Makino HerbariumTokyo Metropolitan UniversityTokyoJapan
  3. 3.Japanese Red Maple Conservation GroupIidaJapan
  4. 4.General Research Center, Ocean Exposition Commemorative Park ManagementNahaJapan
  5. 5.Graduate School of Environment and Information SciencesYokohama National UniversityYokohamaJapan
  6. 6.Tomakomai Experimental ForestHokkaido UniversityTomakomaiJapan

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