Phylogeographic study based on intraspecific sequence variation of chloroplast DNA for the conservation of genetic diversity in the Japanese endangered species Primula sieboldii

Biological Conservation

Volumn 120, Issue 2, 2004, Pages 211-220

  Honjo, M ^a   Ueno, S ^b   Tsumura, Y ^b   Washitani, I ^c   Ohsawa, R ^a  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b FORESTRY AND FOREST PRODUCTS RESEARCH INSTITUTE   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

Chloroplast DNA (cpDNA); Conservation genetics; Haplotype; Intraspecific phylogeography; Restoration activity

Indexed keywords

BIODIVERSITY; DNA; ENDANGERED SPECIES; PHYLOGEOGRAPHY; SPECIES CONSERVATION;

ASIA; EURASIA; FAR EAST; JAPAN;

PRIMULA; PRIMULA SIEBOLDII; PRIMULACEAE;

EID: 3543082230     PISSN: 00063207     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biocon.2004.02.016     Document Type: Article

References (49)

1. Avise J.C. The history and purview of phylogeography: a personal reflection. Molecular Ecology. 7:1998;371-379
2. Barrett S.C.H, Kohn J.R. Genetic and evolutionary consequences of small population size in plants: implications for conservation. Falk D.A, Holsinger K.E. Genetics and Conservation of Rare Plants. 1991;3-30 Oxford University Press, New York
3. Clement M, Posoda D, Crandall K.A. TCS: a computer program to estimate gene genealogies. Molecular Ecology. 9:2000;1657-1659
4. Demesure B, Comps B, Petit R.J. Chloroplast DNA phylogeography of the common beech (Fagus sylvatica L.) in Europe. Evolution. 50:1996;2515-2520
5. Demesure B, Sodzi N, Petit R.J. A set of universal primers for amplification of polymorphic noncoding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology. 4:1995;129-131
6. Dumolin-Lapègue S, Demesure B, Fineschi S, Le Corre V, Petit R.J. Phylogeographic structure of white oaks throughout the European continent. Genetics. 146:1997;1475-1487
7. Environment Agency of Japan., 2000. Threatened Wildlife of Japan, Red Data Book, Vascular Plants, second ed. Environment Agency of Japan, Tokyo (in Japanese)
8. Excoffier L, Smouse P.E, Quattro J.M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 131:1992;479-491
9. Ferris C, King R.A, Vainola R, Hewitt M. Chloroplast DNA recognizes three refugial sources of European oaks and suggests independent eastern and western immigrations to Finland. Heredity. 80:1998;584-593
10. Fujii N, Tomaru N, Okuyama K, Koike T, Mikami T, Ueda K. Chloroplast DNA phylogeography of Fagus crenata (Fagaceae) in Japan. Plant Systematics and Evolution. 232:2002;21-33
11. Fujii N, Ueda K, Watano Y, Shimizu T. Intraspecific sequence variation of chloroplast DNA in Pedicularis chamissonis Steven (Scrophulariaceae) and geographic structuring of the Japanese "alpine" plants. Journal of Plant Research. 110:1997;195-207
12. Fujii N, Ueda K, Watano Y, Shimizu T. Further analysis of intraspecific sequence variation of chloroplast DNA in Primula cuneifolia Ledeb. (Primulaceae): implications for biogeography of the Japanese alpine flora. Journal of Plant Research. 112:1999;87-95
13. Fujii N, Ueda K, Watano Y, Shimizu T. Two genotypes of Pedicularis chamissonis (Scrophulariaceae) distributed at Mt Gassan, Japan: additional genetic and morphological studies. Journal of Plant Research. 114:2001;133-140
14. Hamilton M.B. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology. 8:1999;513-525
15. Hogbin P.M, Peakall R. Evaluation of the contribution of genetic research to the management of the endangered plant Zieria prostrata. Conservation Biology. 13:1999;514-522
16. Ito K. An outline of the flora of Hokkaido. Miyawaki A. Vegetation of Japan. vol. 9:1988;90-96 Hokkaido. Sibundo, Tokyo. (in Japanese)
17. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution. 16:1980;111-120
18. King R.A, Ferris C. Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn. Molecular Ecology. 7:1998;1151-1161
19. Mace G.M, Smith T.B, Bruford M.W, Wayne R.K. An overview of the issues. Smith T.B, Wayne R.K. Molecular Genetic Approaches in Conservation. 1996;3-21 Oxford University Press, New York
20. Matsumura C, Washitani I. Effects of population size and pollinator limitation on seed-set of Primula sieboldii populations in a fragmented landscape. Ecological Research. 15:2000;307-322
21. Murray M.G, Thompson W.F. Rapid isolation of high molecular plant weight DNA. Nucleic Acids Research. 8:1980;4321-4325
22. Nei M. Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the USA. 70:1973;3321-3323
23. Newton A.C, Allnutt T.R, Gillies A.C.M, Lowe A.J, Ennos R.A. Molecular phylogeography, intraspecific variation and the conservation of tree species. Trends in Ecology & Evolution. 14:1999;140-145
24. Ohsawa R, Tsumura Y, Namai H, Washitani I. Isozyme variation of nature-reserve population of Primula sieboldii in Tajimagahara plain. Japanese Journal of Breeding. 41:1991;331-339. (in Japanese with English summary)
25. Ohshima K. The history of straits around the Japanese islands in the late-Quaternary. Quaternary Research. 29:1990;193-208. (in Japanese with English summary)
26. Okaura T, Harada K. Phylogeographical structure revealed by chloroplast DNA variation in Japanese beech (Fagus crenata Blume). Heredity. 88:2002;322-329
27. Robichaux R.H, Friar E.H, Mount D.W. Molecular genetic consequences of a population bottleneck associated with reintroduction of the Mauna Kea silversword (Argyroxiphium sandwicense ssp. sandwicense [Asteraceae]). Conservation Biology. 11:1997;1140-1146
28. Saitou N, Nei M. The neighbor joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution. 4:1987;406-425
29. Schaal B.A, Hayworth D.A, Olsen K.M, Rauscher J.T, Smith W.A. Phylogeographic studies in plants: problems and prospects. Molecular Ecology. 7:1998;465-474
30. Schneider S, Roessli D, Excoffier L. Arlequin, Version 2.000: a software for population genetics data analysis. 2000;Genetics and Biometry Laboratory, University of Geneva, Geneva, Switzerland
31. Soltis D.E, Gitzendanner M.A, Strenge D.D, Soltis P.S. Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Systematics and Evolution. 206:1997;353-373
32. Soltis P.S, Gitzendanner M.A. Molecular systematics and the conservation of rare species. Conservation Biology. 13:1999;471-483
33. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4. 2002;Sinauer Associates, Sunderland, MA
34. Taberlet P, Gielly L, Pautou G, Bouvet J. Universal primers for amplification of three noncoding regions of chloroplast DNA. Plant Molecular Biology. 17:1991;1105-1109
35. Takahashi H, Sato T. Vascular plants of livestock farm of Hokkaido University, Shizunai, Hidaka subprefecture, Hokkaido. Bulletin of the Hokkaido University Farms. 18:2001;33-122. (in Japanese with English summary)
36. Takahashi H, Washitani I, Namai H, Kuroda Y. Conservation biology of Primula sieboldii in the Yatsugatake University Forest. I. Distribution, habitat characteristics and phenology. Bulletin of Tsukuba University Forests. 6:1992;275-286. (in Japanese with English summary)
37. Templeton A.R, Crandall K.A, Sing C.F. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics. 132:1992;619-633
38. Thompson J.D, Higgins D.G, Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequencing weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research. 22:1994;4673-4680
39. Tomaru N, Takahashi M, Tsumura Y, Takahashi M, Ohba K. Intraspecific variation and phylogeographic patterns of Fagus crenata (Fagaceae) mitochondrial DNA. American Journal of Botany. 85:1998;629-636
40. Torii T. Sakurasou. 1985;Nihon-TV, Tokyo. (in Japanese)
41. Uemura, S., Takeda, Y., 1987. Phytogeographical study on the distribution of the main temperate plants composing the natural forests in Hokkaido, Japan. In: Kobe Geobotanical Society (Ed.), Papers on Plant Ecology and Taxonomy to the Memory of Dr Satoshi Nakanishi. Kobe Geobotanical Society, Kobe, pp. 259-269 (in Japanese with English summary)
42. Walter R, Epperson B.K. Geographic pattern of genetic variation in Pinus resinosa: area of greatest diversity is not the origin of postglacial populations. Molecular Ecology. 10:2001;103-111
43. Washitani I. Predicted genetic consequences of strong fertility selection due to pollinator loss in an isolated population of Primula sieboldii. Conservation Biology. 10:1996;59-64
44. Washitani I, Kabaya H. Germination responses to temperature responsible for the seedling emergence seasonability of Primula sieboldii E. Morren in its natural habitat. Ecological Research. 3:1988;9-20
45. Washitani I, Kato M, Nishihiro J, Suzuki K. Importance of queen bumble bees as pollinators facilitating inter-morph crossing in Primula sieboldii. Plant Species Biology. 9:1995;169-176
46. Washitani I, Namai H, Osawa R, Niwa M. Species biology of Primula sieboldii for the conservation of its lowland-habitat population: I. Inter-clonal variations in the flowering phenology, pollen load and female fertility components. Plant Species Biology. 6:1991;27-37
47. Washitani I, Osawa R, Namai H, Niwa M. Patterns of female fertility in heterostylous Primula sieboldii under severe pollinator limitation. Journal of Ecology. 82:1994;571-579
48. Wolf P.G, Sinclair R.B. Highly differentiated populations of the narrow endemic plant Maguire primrose (Primula maguirei). Conservation Biology. 11:1997;375-381
49. Yamazaki T. Primula. Iwatsuki K, Yamazaki T, Boufford D.E, Ohba H. Flora of Japan 3a. 1993;87-94 Kodansha, Tokyo