Comparative phylogeography of four component species of deciduous broad-leaved forests in Japan based on chloroplast DNA variation

Journal of Plant Research

Volumn 125, Issue 2, 2012, Pages 207-221

  Iwasaki, Takaya ^a,b   Aoki, Kyoko ^c   Seo, Akihiro ^d   Murakami, Noriaki ^e  

^a CHIBA UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c KYOTO UNIVERSITY   (Japan)

^d RESEARCH INSTITUTE FOR HUMANITY AND NATURE   (Japan)

^e TOKYO METROPOLITAN UNIVERSITY   (Japan)

Author keywords

Chloroplast DNA; Deciduous broad leaved forest; Glacial refugia; Intraspecific variation; Japanese archipelago; Phylogeography

Indexed keywords

CHLOROPLAST DNA; PLANT DNA; SPACER DNA;

ANGIOSPERM; ARTICLE; CHEMISTRY; COMPARATIVE STUDY; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; JAPAN; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGEOGRAPHY; PLANT LEAF; SPECIES DIFFERENCE; TREE;

ANGIOSPERMS; BASE SEQUENCE; DNA, CHLOROPLAST; DNA, INTERGENIC; DNA, PLANT; GENETIC VARIATION; HAPLOTYPES; JAPAN; MOLECULAR SEQUENCE DATA; PHYLOGEOGRAPHY; PLANT LEAVES; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TREES;

CARPINUS LAXIFLORA; EUONYMUS; MAGNOLIA HYPOLEUCA; MAGNOLIACEAE; PADUS;

EID: 84857901991     PISSN: 09189440     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10265-011-0428-8     Document Type: Article

References (66)

1. Abbott RJ, Smith LC, Milne RI, Crawford RMM, Wolff K, Balfour J (2000) Molecular analysis of plant migration and refugia in the Arctic. Science 289: 1343-1346.
2. Aoki K, Suzuki T, Hu T, Murakami N (2004) Phylogeography of the component species of broad-leaved evergreen forests in Japan, based on chloroplast DNA variation. J Plant Res 117: 77-94.
3. Avise JC (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge.
4. Bivand R (2009) The spdep package. Comprehensive R archive network, version 0. 4-34.
5. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9: 1657-1659.
6. Corriveau JL, Coleman AW (1988) Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. Am J Bot 75: 1443-1458.
7. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11-15.
8. Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Mol Ecol 11: 2571-2581.
9. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3. 0: An integrated software package for population genetics data analysis. Evol Bioinforma Online 1: 47-50.
10. Fujii N, Senni K (2006) Phylogeography of Japanese alpine plants: biogeographic importance of alpine region of Central Honshu in Japan. Taxon 55: 43-52.
11. Fujii N, Ueda K, Watano Y, Shimizu T (1997) Intraspecific sequence variation of chloroplast DNA in Pedicularis chamissonis Steven (Scrophulariaceae) and geographic structuring of the Japanese "Alpine" plants. J Plant Res 110: 195-207.
12. Fujii N, Tomaru N, Okuyama K, Koike T, Mikami T, Ueda K (2002) Chloroplast DNA phylogeography of Fagus crenata (Fagaceae) in Japan. Plant Syst Evol 232: 21-33.
13. Godbout J, Jaramillo-Correa JP, Beaulieu J, Bousquet J (2005) A mitochondrial DNA minisatellite reveals the postglacial history of jack pine (Pinus banksiana), a broad-range North American conifer. Mol Ecol 141: 3497-3512.
14. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
15. Hamilton MB (1999) Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol Ecol 8: 521-523.
16. Hamrick JL, Godt MJW (1989) Allozyme diversity in plant species. In: Brown AHD, Clegg MT, Kahler AL, Weir BS (eds) Plant population genetics, breeding, and genetic resources. Sinauer, Sunderland, pp 43-63.
17. Hamrick JL, Godt MJW, Sherman-Broyles SL (1992) Factors influencing levels of genetic diversity in woody plant species. New For 6: 95-124.
18. Heuertz M, Fineschi S, Anzidei M, Pastorelli R, Salvini D, Paule L, Frascaria-Lacoste N, Hardy OJ, Vekemans X, Vendramin GG (2004) Chloroplast DNA variation and postglacial recolonization of common ash (Fraxinus excelsior L.) in Europe. Mol Ecol 13: 3437-3452.
19. Hewitt GM (1996) Some genetic consequences of ice ages, and their role, in divergence and speciation. Biol J Linn Soc Lond 58: 247-276.
20. Hewitt GM (2000) The genetic legacy of the Quaternary ice ages. Nature 405: 907-913.
21. Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Philos Trans R Soc Lond B 359: 183-195.
22. Hiraoka K, Tomaru N (2009) Genetic divergence in nuclear genomes between populations of Fagus crenata along the Japan Sea and Pacific sides of Japan. J Plant Res 122: 269-282.
23. Ikeda H, Setoguchi H (2007) Phylogeography and refugia of the Japanese endemic alpine plant, Phyllodoce nipponica Makino (Ericaceae). J Biogeogr 34: 169-176.
24. Ingvarsson PK, Ribstein S, Taylor DR (2003) Molecular evolution of insertions and deletions in the chloroplast DNA genome of silence. Mol Biol Evol 20: 1737-1740.
25. Iwasaki T, Aoki K, Seo A, Murakami N (2006) Intraspecific sequence variation of chloroplast DNA among the component species of deciduous broad-leaved forests in Japan. J Plant Res 119: 539-552.
26. Kamei T, Research Group for the Biogeography from Würm Glacial (1981) Fauna and flora of the Japanese islands in the last glacial time. Quaternary Res 20: 191-205 (in Japanese with English abstract).
27. Kanno M, Yokoyama J, Suyama Y, Ohyama M, Itoh T, Suzuki M (2004) Geographical distribution of two haplotypes of chloroplast DNA in four oak species (Quercus) in Japan. J Plant Res 117: 311-317.
28. Kira T (1977) A climatological interpretation of Japanese vegetation zones. In: Miyawaki A, Tüxen R (eds) Vegetation science and environmental protection. Maruzen Co, Ltd, Tokyo, pp 21-30.
29. Kira T (1991) Forest ecosystems of east and southeast Asia in a global perspective. Ecol Res 6: 185-200.
30. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
31. Magri D, Vendramin GG, Comps B, Dupanloup I, Geburek T, Gömöry D, Latałowa M, Litt T, Paule T, Roure JM, Tantau I, Knaap WO, Petit RJ, Beaulieu J (2006) A new scenario for the Quaternary history of European beech populations: palaeobotanical evidence and genetic consequences. New Phytol 171: 199-221.
32. McCauley DE (1995) The use of chloroplast DNA polymorphism in studies of gene flow in plants. Trends Ecol Evol 10: 198-202.
33. McCune B, Mefford MJ (1999) PC-ORD. Multivariate analysis of ecological communities. MjM Software Design, Gleneden Beach, OR, USA.
34. McCune B, Grace JB, Urban DL (2002) Analysis of ecological communities. MjM Software Design, Gleneden Beach, OR, USA.
35. McLachlan JS, Clark JS (2004) Reconstructing historical ranges with fossil data at continental scales. For Ecol Manag 197: 139-147.
36. Moran PAP (1950) Notes on continuous stochastic phenomena. Biometrika 37: 17-23.
37. Murata G (1972) Taxonomical notes 10. Acta Phytotax Geobot 25: 45-53 (in Japanese).
38. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York.
39. Newton AC, Allnutt TR, Gillies ACM, Lowe AJ, Ennos RA (1999) Molecular phylogeography, intraspecific variation and the conservation of tree species. Trends Ecol Evol 14: 140-145.
40. Nishizawa T, Watano Y (2000) Primer pairs suitable for PCR-SSCP analysis of chloroplast DNA in angiosperms. J Phytogeogr Taxon 48: 63-66.
41. Ohi T, Wakabayashi M, Wu S, Murata J (2003) Phylogeography of Stachyurus praecox (Stachyuraceae) in the Japanese archipelago based on chloroplast DNA haplotypes. J Jpn Bot 78: 1-14.
42. Ohta Y, Yonekura N (1987) Coastal line. In: Japan Association for Quaternary Research (ed) Quaternary maps of Japan. University of Tokyo Press, Tokyo, pp 70-72 (in Japanese).
43. Okaura T, Harada K (2002) Phylogeographical structure revealed by chloroplast DNA variation in Japanese beech (Fagus crenata Blume). Heredity 88: 322-329.
44. Okaura T, Quang ND, Ubukata M, Harada K (2007) Phylogeographic structure and late Quaternary population history of the Japanese oak Quercus mongolica var. crispula and related species revealed by chloroplast DNA variation. Genes Genet Syst 82: 465-477.
45. Ono Y (1984) Late glacial paleoclimate reconstructed from glacial and periglacial landforms in Japan. Geogr Rev Jpn Ser B 57: 80-100 (in Japanese).
46. Peakall R, Smouse PE (2006) GENEALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6: 288-295.
47. Petit RJ, Aguinagalde I, Beaulieu J, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, Mohanty A, Muller-Starck G, Demesure-Musch B, Palme A, Martin JP, Rendell S, Vendramin GG (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300: 1563-1565.
48. Pons O, Petit RJ (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144: 1237-1245.
49. R Development Core Team (2010) R: a language and environment for statistical computing. R Foundation for Statistical Computing. http://www. P-project. org/.
50. Setoguchi H, Ohba H (1995) Phylogenetic relationships in Crossostylis (Rhizophoraceae) inferred from restriction site variation of chloroplast DNA. J Plant Res 108: 87-92.
51. Simmons MP, Ochoterena H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49: 369-381.
52. Sneath PHA, Sokal PR (1973) Numerical taxonomy: the principles and practice of numerical classification. Freeman WH, San Francisco.
53. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17: 1105-1109.
54. Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF (1998) Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol 7: 453-464.
55. 14C yr BP. J Biogeogr 27: 665-683.
56. Takahashi T, Tani N, Taira H, Tsumura Y (2005) Microsatellite markers reveal high allelic variation in natural populations of Cryptomeria japonica near refugial areas of the last glacial period. J Plant Res 118: 83-90.
57. Terachi T (1993) Structural alterations of chloroplast genome and their significance to the higher plant evolution. Bull Inst Natl Land Util Dev Kyoto Sangyo Univ 14: 138-148 (in Japanese with English summary).
58. Tomaru N, Mitsutsuji T, Takahashi M, Tsumura Y, Uchida K, Ohba K (1997) Genetic diversity in Fagus crenata (Japanese beech): influence of the distribution shift during the late-Quaternary. Heredity 78: 241-251.
59. Tomaru N, Takahashi M, Tsumura Y, Takahashi M, Ohba K (1998) Intraspecific variation and phylogeographic patterns of Fagus crenata (Fagaceae) mitochondrial DNA. Am J Bot 85: 629-636.
60. Tremblay NO, Schoen DJ (1999) Molecular phylogeography of Dryas integrifolia: glacial refugia and postglacial recolonization. Mol Ecol 8: 1187-1198.
61. Tsukada M (1982a) Late-quaternary shift of Fagus distribution. J Plant Res 95: 203-217.
62. Tsukada M (1982b) Cryptomeria japonica: glacial refugia and late-glacial and postglacial migration. Ecology 63: 1091-1105.
63. Tsukada M (1988) Japan. In: Huntley B, Webb T III (eds) Vegetation history. Kluwer, London, pp 459-518.
64. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: 256-276.
65. 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: 9054-9058.
66. Yasuda Y, Miyoshi N (1998) Vegetation history in the Japanese archipelago. Asakura, Tokyo (in Japanese).