Conservation Genetics

, Volume 12, Issue 2, pp 491–501 | Cite as

Genetic structure of the critically endangered plant Tricyrtis ishiiana (Convallariaceae) in relict populations of Japan

  • Hiroaki SetoguchiEmail author
  • Yuki Mitsui
  • Hajime Ikeda
  • Naofumi Nomura
  • Atsushi Tamura
Research Article


Tricyrtis ishiiana is a relic endemic plant taxon of the Convallariaceae that inhabits two nearby gorges in Kanagawa Prefecture, Japan. The distribution range and number of populations are thought to have been reduced to the present refugial populations during the Quaternary climatic oscillations. Because of its showy flowers, this plant has faced illegal removal from its natural habitats for horticultural use and has been designated a critically endangered species (class IA). In this study, we analyzed the genetic structure of the relict populations of T. ishiiana in order to contribute to the conservation strategies of the prefectural government. Our analyses of nine nuclear microsatellite loci detected high genetic diversity (HE = 0.704 and HO = 0.541) for the two populations. The two populations were slightly differentiated (RST = 0.032), accompanied by faint substructure across the populations (K = 3). In addition, each population exhibited spatial genetic structuring. The relatively low inbreeding coefficient for both populations together (FIS = 0.233) and each population separately (FIS = 0.217–0.246) may be attributable to crossing among descendants within a population along with occasional gene flow between the populations. These results suggested that the extant populations have not experienced a severe bottleneck. The two extant populations were genetically differentiated at a very low level, accompanied by occasional pollen flow via pollinators and/or seed dispersal by gravity in the mountainous environment. Occasional gene exchange between the populations has allowed T. ishiiana to harbor high genetic diversity despite being a relic plant confined to two small refugial populations.


Convallariaceae Gene flow Microsatellite Refugia Tricyrtis ishiiana 



We are grateful to Ms. Akiko Sakai (Kanagawa Prefecture Natural Environment Conservation Center), and Asuka Noda, Kanako Sugahara and Tomomi Dan (Kyoto University) for their cooperation in collecting materials and extracting DNA, respectively. Prof. Masayuki Maki (Tohoku University) kindly showed us his unpublished data (currently in press). This study was supported by a grant for Conservation Genetics for Endangered Plants from Kanagawa Prefecture Natural Environment Conservation Center.


  1. Cornuet JM, Luikart G (1996) Description and evaluation of two tests for detecting recent bottlenecks. Genetics 144:2001–2014PubMedGoogle Scholar
  2. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from plant tissue. Focus 12:13–15Google Scholar
  3. Edwards AL, Wyatt R (1994) Population genetics of the rare Asclepias texana and its widespread sister species, A. perennis. Syst Bot 19:291–307CrossRefGoogle Scholar
  4. El Mousadik A, Petit RJ (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco. Theor Appl Genet 92:832–839CrossRefGoogle Scholar
  5. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620PubMedCrossRefGoogle Scholar
  6. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50PubMedGoogle Scholar
  7. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587PubMedGoogle Scholar
  8. Godt MJW, Walker J, Hamrick JL (1997) Genetic diversity in the endangered lily Harperocallis flava and a close relative, Tofieldia racemosa. Conser Biol 11:361–366 CrossRefGoogle Scholar
  9. Goudet J (1995) Fstat version 1.2: a computer program to calculate F statistics. J Hered 86:485–486Google Scholar
  10. Goudet J, Raymond M, De-Meeus T, Rousset F (1996) Testing differentiation in diploid populations. Genetics 144:1933–1940PubMedGoogle Scholar
  11. Hardy OJ, Vekemans X (2002) SPAGEDI: a versatile computer program to analyze spatial genetic structure at the individual or population level. Mol Ecol Notes 2:618–620CrossRefGoogle Scholar
  12. Ikeda H, Senni K, Fujii N, Setoguchi H (2006) Refugia of Potentilla matsumurae (Rosaceae) located at high mountains in the Japanese archipelago. Mol Ecol 15:3731–3740PubMedCrossRefGoogle Scholar
  13. Japan Society of Plant Taxonomists (1993) Red Data Book: Japanese endangered plants. Nousonbunka-sha, Tokyo (in Japanese)Google Scholar
  14. Linhart YB, Permoli AC (1993) Genetic variation in Altes acaulis and its relative, the narrow endemic A. humilis (Apiaceae). Am J Bot 80:598–605CrossRefGoogle Scholar
  15. Luikart G, Allendorf FW, Cornuet JM, Sherwin WB (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. J Hered 89:238–247PubMedCrossRefGoogle Scholar
  16. Lumaret R, Mir C, Michaud H, Raynal V (2002) Phylogeograpical variation of chloroplast DNA in holm oak (Quercus ilex L.). Mol Ecol 11:2327–2336PubMedCrossRefGoogle Scholar
  17. Maki Y, Morita H, Oiki S, Takahashi H (1999) The effect of geographic range and dichogamy on genetic variability and population genetic structure in Tricyrtis section Flavae (Liliaceae). Am J Bot 86:287–292CrossRefGoogle Scholar
  18. Maruyama T, Fuerst PA (1985) Population bottlenecks and non equilibrium models in population genetics. II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics 111:675–678PubMedGoogle Scholar
  19. Ministry of the Environment of Japan (2000) Threatened wildlife of Japan, Red Data Book, vol 8, 2nd ed (vascular plants). Japan Wildlife Research Center, Tokyo (in Japanese)Google Scholar
  20. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  21. Palmé AE, Vendramin GG (2002) Chloroplast DNA variation, postglacial recolonization and hybridization in hazel, Corylus avellana. Mol Ecol 11:1769–1779PubMedCrossRefGoogle Scholar
  22. Peakall R, Smouse PE (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295CrossRefGoogle Scholar
  23. Petit RJ, Brewer S, Bordács S, Burg K, Cheddadi R, Coart E, Cottrell J, Csaikl UM, van Dam B, Deans JD, Espinel S, Fineschi S, Finkeldey R, Glaz I, Goicoechea PG, Jensen JS, König AO, Lowe AJ, Madsen SF, Mátyás G, Munro RC, Popescu F, Slade D, Tabbener H, de Vries SGM, Ziegenhagen B, de Beaulieu JL, Kremer A (2002) Identification of refugia and post-glacial colonization routes of European white oaks based on chloroplast DNA and fossil pollen evidence. For Ecol Manag 156:49–74CrossRefGoogle Scholar
  24. Petit RJ, Aguinagalde I, de Beaulieu JL, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, Mohanty A, Muller-Starck GM, Demesure-Musch B, Palme A, Martin JP, Rendell S, Vendramin GG (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300:1563–1565PubMedCrossRefGoogle Scholar
  25. Piry S, Luikart G, Cornuet JM (1999) Bottleneck: a computer program for detecting recent reductions in the effective population size using allele frequency data. J Hered 90:502–503CrossRefGoogle Scholar
  26. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  27. Purdy BG, Bayer RJ (1995a) Allozyme variation in the Athabasca sand dune endemic, Salix silicicola, and the closely related widespread species, S. alaxensis. Syst Bot 20:179–190CrossRefGoogle Scholar
  28. Purdy BG, Bayer RJ (1995b) Genetic diversity in the tetraploid sand dune endemic Deshampia mackenzieana and its widespread progenitor D. cespitosa (Poaceae). Am J Bot 82:121–130CrossRefGoogle Scholar
  29. Purdy BG, Bayer RJ (1996) Genetic variation in populations of the endemic Achillea millefolium ssp. megacephala from the Athabasca sand dunes and the widespread ssp. lanulosa in western North America. Can J Bot 74:1138–1146CrossRefGoogle Scholar
  30. Qiu YX, Sun Y, Zhang XP, Lee J, Fu CX, Comes HP (2009) Molecular phylogeography of East Asian Kirengeshoma (Hydrangeaceae) in relation to quaternary climate change and landbridge configurations. New Phytol 183:480–495PubMedCrossRefGoogle Scholar
  31. Queller DC, Goodnight KF (1989) Estimating relatedness using genetic markers. Evol Int J Org Evol 43:258–275CrossRefGoogle Scholar
  32. Rousset F (1996) Equilibrium values of measures of population subdivision for stepwise mutation processes. Genetics 142:1357–1362PubMedGoogle Scholar
  33. Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219–1228PubMedGoogle Scholar
  34. Schönswetter P, Stehlik I, Holderegger R, Tribsch A (2005) Molecular evidence for glacial refugia of mountain plants in the Europe Alps. Mol Ecol 14:3547–3555PubMedCrossRefGoogle Scholar
  35. Setoguchi H, Ohba H (1995) Phylogenetic relationships in Crossostylis inferred from restriction site variation of chloroplast DNA. J Plant Res 108:87–92CrossRefGoogle Scholar
  36. Setoguchi H, Mitsui Y, Ikeda H, Nomura N, Tamura A (2009) Development and characterization of microsatellite loci in the endangered Tricyrtis ishiiana (Convallariaceae), a local endemic plant in Japan. Conserv Genet 10:705–707CrossRefGoogle Scholar
  37. Sherman-Broyles SL, Gibson JP, Hamrick JL, Bucher MA, Gibson MJ (1992) Compariosn of allozyme diversity among rare and widespread Rhus species. Syst Bot 17:551–559CrossRefGoogle Scholar
  38. Slatkin M (1995) A measure of population subdivision based on microsatellite allele frequency. Genetics 139:457–462PubMedGoogle Scholar
  39. Takahashi H (1993) Floral biology of Tricyrtis macranthopsis Masamune and T. ishiiana (Kitagawa et T. Koyama) Ohwi et Okuyama (Liliaceae). Acta Phytotaxonomica et Geobotanica 44:141–150Google Scholar
  40. Takahashi Y, Takahashi H, Maki Y Comparison of genetic variation and differentiation using microsatellite markers among three rare threatened and one widespread toad lily species of Tricyrtis section Flavae (Convallariaceae) in Japan. Plant Species Biol (in press)Google Scholar
  41. Watterson GA (1978) The homozygosity test of neutrality. Genetics 88:405–417PubMedGoogle Scholar
  42. Watterson GA (1986) The homozygosity test after a change in population size. Genetics 112:899–907PubMedGoogle Scholar
  43. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370CrossRefGoogle Scholar
  44. Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163:1177–1191PubMedGoogle Scholar
  45. Wright S (1943) Isolation by distance. Genetics 28:114–138PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Hiroaki Setoguchi
    • 1
    Email author
  • Yuki Mitsui
    • 1
  • Hajime Ikeda
    • 1
  • Naofumi Nomura
    • 1
  • Atsushi Tamura
    • 2
  1. 1.Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
  2. 2.Kanagawa Prefecture Natural Environment Conservation CenterAtsugiJapan

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