Nuclear and chloroplast microsatellite analysis of Abies sachalinensis regeneration on fallen logs in a subboreal forest in Hokkaido, Japan

Molecular Ecology

Volumn 17, Issue 12, 2008, Pages 2948-2962

  Lian, Chunlan ^a   Goto, Susumu ^a   Kubo, Takuya ^b   Takahashi, Yasuo ^a   Nakagawa, Masahiko ^c   Hogetsu, Taizo ^d  

^a UNIVERSITY OF TOKYO   (Japan)

^b HOKKAIDO UNIVERSITY   (Japan)

^c HOKKAIDO FORESTRY RESEARCH INSTITUTE   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

Author keywords

Abies sachalinensis; cpSSR; Dispersal; Genetic structure; Microhabitat; Recruitment; Safe site

Indexed keywords

CHLOROPLAST DNA; MICROSATELLITE DNA;

ABIES; ARTICLE; CELL NUCLEUS; ECOSYSTEM; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; JAPAN; PHYSIOLOGY; REGENERATION; TREE;

ABIES; CELL NUCLEUS; DNA, CHLOROPLAST; ECOSYSTEM; GEOGRAPHY; JAPAN; MICROSATELLITE REPEATS; REGENERATION; TREES; VARIATION (GENETICS);

ABIES; ABIES SACHALINENSIS; CONIFEROPHYTA;

EID: 44849134140     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.03802.x     Document Type: Article

References (70)

1. Aldrich PR, Hamrick JL (1998) Reproductive dominance of pasture trees in a fragmented tropical forest mosaic. Science, 281, 103 105.
2. Asakawa S (1981) The Seeds of Japanese Trees - Conifer Trees (in Japanese). Japanese Forest Tree Breeding Association, Tokyo, Japan.
3. Asuka Y, Tomaru N, Munehara Y et al 2005) Half-sib family structure of Fagus crenata saplings in an old-growth beech-dwarf bamboo forest. Molecular Ecology, 14, 2565 2575.
4. Bolker B, Okuyama T, Bjorndal K, Bolten A (2007) Incorporating multiple mixed stocks in mixed stock analysis: many-to-many analyses. Molecular Ecology, 16, 685 695.
5. Burczyk J, Prat D (1997) Male reproductive success in Pseudotsuga menziesii (Mirb.) Franco: the effects of spatial structure and flowering characteristics. Heredity, 79, 638 647.
6. Clark JS (2005) Why environmental scientists are becoming Bayesians. Ecology Letters, 8, 2 14.
7. Clark JS, Gelfand AE (2006) Hierarchical Modelling for the Environmental Sciences. Oxford University Press, Oxford, UK.
8. Clark JS, Silman M, Kern R, HillerRisLambers J (1999) Seed dispersal near and far: patterns across temperate and tropical forests. Ecology, 80, 1475 1494.
9. Dow BD, Ashley MV (1996) Microsatellite analysis of seed dispersal and parentage of saplings in bur oak, Quercus macrocarpa. Molecular Ecology, 5, 615 627.
10. Epperson B, Alvarez-Buylla E (1997) Limited seed dispersal and genetic structure in life stages of Cecropia obtusifolia. Evolution, 51, 275 282.
11. Gelman A, Carlin J, Stern H, Rubin D (2004) Bayesian Data Analysis, 2nd edn. Chapman and Hall CRC, London, UK.
12. Godoy JA, Jordano P (2001) Seed dispersal by animals: exact tracking of the source trees with endocarp DNA microsatellites. Molecular Ecology, 10, 2275 2283.
13. González-Maritínez SC, Burczyk J, Nathan R et al 2006) Effective gene dispersal and female reproductive success in Mediterranean maritime pine (Pinus pinaster Aiton). Molecular Ecology, 15, 4577 4588.
14. Goto S, Shimatani K, Yoshimaru H, Takahashi Y (2006) Fat-tailed gene flow in the dioecious canopy tree species Fraxinus mandshurica var. japonica revealed by microsatellites. Molecular Ecology, 15, 2985 2996.
15. Goudet J (2001) fstat, A Program to Estimate and Test Gene Diversities and Fixation Indexes (Version 2.9.3). Université de Lausanne, Dorigny, Switzerland. Avaliable from URL: http://www2.unil.ch/popgen/softwares/fstat.htm.
16. Grivet D, Smouse P, Sork V (2005) A novel approach to an old problem: tracking dispersed seeds. Molecular Ecology, 14, 3585 3595.
17. Hamrick JL, Nason JD (1996) Consequences of dispersal in plants. In : Population Dynamics in Ecological Space and Time (eds Rhodes OE, Chesser RK, Smith MH), pp. 203 236. University of Chicago Press, Chicago, Illinois, USA.
18. Hamrick JL, Murawski DA, Nason JD (1993) The influence of seed dispersal mechanisms on the genetic structure of tropical tree populations. Plant Ecology, 107, 281 297.
19. Hardesty BD, Dick CW, Kremer A, Hubbell S, Bermingham E (2005) Spatial genetic structure of Simarouba amara aubl. (simaroubaceae), a dioecious, animal-dispersed Neotropical tree, on Barro Colorado Island, Panama. Heredity, 95, 290 297.
20. Hardesty B, Hubbell S, Bermingham E (2006) Genetic evidence of frequent long distance recruitment in a vertebrate-dispersed tree. Ecology Letters, 9, 516 525.
21. Harmon M, Franklin J (1989) Tree seedlings on logs in Picae-Tsuga forests of Oregon and Washington. Ecology, 70, 48 59.
22. Hiura T, Sano J, Konno Y (1996) Age structure and response to fine-scale disturbances of Abies sachalinensis, Picea jezoensis, Picea glehnii, and Betula ermanii growing under the influence of a dwarf bamboo understory in northern Japan. Canadian Journal of Forest Research, 26, 289 297.
23. Iijima H, Shibuya M, Hideyuki S (2007) Effects of surface and light conditions of fallen logs on the emergence and survival of coniferous seedlings and saplings. Journal of Forest Research, 12, 262 269.
24. Isagi Y, Kanazashi T, Suzuki W, Tanaka H, Abe T (2000) Microsatellite analysis of the regeneration process of Magnolia obovata Thunb. Heredity, 84, 143.
25. Jones F, Chen J, Weng GJ, Hubbell S (2005) A genetic evaluation of seed dispersal in the Neotropical tree Jacaranda copaia (Bignoniaceae). American Naturalist, 166, 543 555.
26. Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16, 1099 1106.
27. Kalisz S, Nason J, Hanzawa F, Tonsor S (2001) Spatial population genetic structure in Trillium grandiflorum: the roles of dispersal, mating, history, and selection. Evolution, 55, 1560 1568.
28. Kameyama Y, Isagi Y, Nakagoshi N (2001) Patterns and levels of gene flow in Rhododendron metternichii var. hondoense revealed by microsatellite analysis. Molecular Ecology, 10, 205 216.
29. Knowles P (1991) Spatial genetic-structure within 2 natural stands of black spruce (Picea mariana (Mill) (Bsp). Silvae Genetica, 40, 13 19.
30. Kubota Y, Konno Y, Hiura T (1994) Stand structure and growth patterns of understorey trees in a coniferous forest, Taisetsuzan National Park, northern Japan. Ecological Research, 9, 333 341.
31. Latta R, Linhart Y, Fleck D, Elliot M (1998) Direct and indirect estimates of seed versus pollen movement within a population of Ponderosa pine. Evolution, 52, 61 67.
32. Latouche-Halle C, Romboer A, Bandou E, Caron H, Kremer A (2004) Long-distance pollen flow and tolerance to selfing in neotropical tree species. Molecular Ecology, 13, 1055 1064.
33. Lee PM (2004) Bayesian Statistics: An Introduction, 3rd edn. Arnold Publishing, New York.
34. Lian CL, Oishi R, Miyashita N et al 2003) Genetic structure and reproduction dynamics of Salix reinii during primary succession on Mount Fuji, as revealed by nuclear and chloroplast microsatellite analysis. Molecular Ecology, 12, 609 618.
35. Lian CL, Goto S, Hogetsu T (2007) Microsatellite markers for Sachalin fir (Abies sachalinensis Masters). Molecular Ecology Notes, 7, 896 898.
36. Liepelt S, Kuhlenkamp V, Anzidei M, Vendramin GG, Ziegenhagen B (2001) Pitfalls in determining size homoplasy of microsatellite loci. Molecular Ecology Notes, 1, 332 335.
37. Loiselle BA, Sork VL, Nason J, Graham C (1995) Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). American Journal of Botany, 82, 1420 1425.
38. Loveless MD, Hamrick JL (1984) Ecological determinants of genetic structure in plant populations. Annual Review of Ecology and Systematics, 15, 65 95.
39. Lusk CH, Kelly C (2003) Interspecific variation in seed size and safe sites in a temperate rain forest. New Phytologist, 158, 535 541.
40. McCullough HA (1948) Plant succession on fallen logs in a virgin spruce-fir forest. Ecology, 29, 508 513.
41. Meagher T, Thompson E (1987) Analysis of parentage for naturally established seedlings of Chamaelirium Luteum (Liliaceae). Ecology, 68, 803 812.
42. Nagaike TK, Kubota Y, Watanabe N (1999) The effects of selective logging on stand structure and the regeneration of subboreal forests in Hokkaido, northern Japan. Journal of Forest Research, 4, 41 45.
43. Nakagawa M, Kurahashi A, Kaji M, Hogetsu T (2001) The effects of selection cutting on regeneration of Picea jezoensis and Abies sachalinensis in the sub-boreal forests of Hokkaido, northern Japan. Forest Ecology and Management, 146, 15 23.
44. Nakagawa M, Kurahashi A, Kaji M, Hogetsu T (2003) The regeneration characteristics of Picea jezoensis and Abies sachalinensis on cut stumps in the sub-boreal forests of Hokkaido Tokyo University Forest. Forest Ecology and Management, 180, 353 359.
45. Narukawa Y, Yamamoto S (2002) Effects of dwarf bamboo (Sasa sp.) and forest floor microsites on conifer seedling recruitment in a subalpine forest, Japan. Forest Ecology and Management, 163, 61 70.
46. Narukawa Y, Iida S, Tanouchi H, Abe S, Yamamoto SI (2003) State of fallen logs and the occurrence of conifer seedlings and saplings in boreal and subalpine old-growth forests in Japan. Ecological Research, 18, 267 277.
47. O'Hanlon-Manners DL, Kotanen PM (2004) Logs as refuges from fungal pathogens for seeds of eastern hemlock (Tsuga canadensis). Ecology, 85, 284 289.
48. Ogasawara S, Takahashi Y, Kurahashi A, Hamatani T (1981) Seed dispersal of Abies sachalinensis, Acer mono and Tilia japonica. Transactions of the Meeting in Hokkaido Branch of the Japanese Forestry Society, 29, 65 67 (in Japanese).
49. Palo J, O'hara R, Laugen A et al 2003) Latitudinal divergence of common frog (Rana temporaria) life history traits by natural selection: evidence from a comparison of molecular and quantitative genetic data. Molecular Ecology, 12, 1963 1978.
50. Peakall R, Smouse P (2006) genalex 6: genetic analysis in Excel, population genetic software for teaching and research. Molecular Ecology Notes, 6, 288 295.
51. R Development Core Team (2006) r: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
52. Raymond M, Rousset F (1995) genepop (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86, 248 249.
53. Robledo-Arnuncio JJ, Gil L (2005) Patterns of pollen dispersal in a small population of Pinus sylvestris L. revealed by total-exclusion paternity analysis. Heredity, 94, 13 22.
54. Sato H, Hiura T (1998) Estimation of overlapping seed shadows in a northern mixed forest. Forest Ecology and Management, 104, 69 76.
55. Sato T, Isagi Y, Sakio H, Osumi K, Goto S (2006) Effect of gene flow on spatial genetic structure in the riparian canopy tree Cercidiphyllum japonicum revealed by microsatellite analysis. Heredity, 96, 79 84.
56. Schnabel A, Nason JD, Hamrick JL (1998) Understanding the population genetic structure of Gleditsia triacanthos L. seed dispersal and variation in female reproductive success. Molecular Ecology, 7, 819 832.
57. Schoen DJ, Stewart SC (1986) Variation in Male Reproductive Investment and Male Reproductive Success in White Spruce. Evolution, 40, 1109 1120.
58. Spiegelhalter D, Thomas A, Best N, Lunn D (2003) winbugs user manual. MRC Biostatistics Unit, Cambridge, UK.
59. Sturtz S, Ligges U, Gelman A (2005) r2winbugs: a package for running winbugs from r. Journal of Statistical Software, 12, 1 16.
60. Suzuki E (1987) Regeneration process of coniferous forests in northern Hokkaido 1. Abies sachalinensis forest and Picea glehnii forest. Ecological Research, 2, 61 75.
61. Takahashi M, Sakai Y, Ootomo R, Shiozaki M (2000) Establishment of tree seedlings and water-soluble nutrients in coarse woody debris in an old-growth Picea-Abies forest in Hokkaido, northern Japan. Canadian Journal of Forest Research-Revue Canadienne de Recherche Forestiere, 30, 1148 1155.
62. Troupin D, Nathan R, Vendramin GG (2006) Analysis of spatial genetic structure in an expanding Pinus halepensis population reveals development of fine-scale genetic clustering over time. Molecular Ecology, 15, 3617 3630.
63. Vekemans X, Hardy OJ (2004) New insights from fine-scale spatial genetic structure analyses in plant populations. Molecular Ecology, 13, 921 935.
64. Vendramin GG, Ziegenhagen B (1997) Characterization and inheritance of polymorphic plastid microsatellites in Abies. Genome, 40, 857 864.
65. Vendramin GG, Lelli L, Rossi P, Morgante M (1996) A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Molecular Ecology, 5, 595 598.
66. Vendramin GG, Degen B, Petit RJ et al 1999) High level of variation at Abies alba chloroplast microsatellite loci in Europe. Molecular Ecology, 8, 1117 1126.
67. Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358 1370.
68. Xie CY, Knowles P (1991) Spatial genetic substructure within natural populations of jack pine (Pinus banksiana). Canadian Journal of Botany, 69, 547 551.
69. Yamaji K, Fukushi Y, Hashidoko Y, Yoshida T, Tahara S (2001) Penicillium fungi from Picea glehnii seeds protect the seedlings from damping-off. New Phytologist, 152, 521 531.
70. Ziegenhagen B, Scholz F, Madaghiele A, Vendramin GG (1998) Chloroplast microsatellites as markers for paternity analysis in Abies alba. Canadian Journal of Forest Research, 28, 317 321.